Starting phenix.real_space_refine on Sun Sep 29 00:23:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f93_31496/09_2024/7f93_31496.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f93_31496/09_2024/7f93_31496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f93_31496/09_2024/7f93_31496.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f93_31496/09_2024/7f93_31496.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f93_31496/09_2024/7f93_31496.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f93_31496/09_2024/7f93_31496.cif" } resolution = 3.6 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= 0.001 sd= 0.047 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 96 5.16 5 C 14460 2.51 5 N 3048 2.21 5 O 3204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 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: 20808 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "B" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "C" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "D" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "E" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "F" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "G" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "H" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "I" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "J" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "K" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "L" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'C14': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'C14': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'C14': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "D" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'C14': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'C14': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "F" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'C14': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'C14': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "H" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'C14': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "I" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'C14': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "J" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'C14': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "K" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'C14': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "L" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'C14': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 14.49, per 1000 atoms: 0.70 Number of scatterers: 20808 At special positions: 0 Unit cell: (97.8945, 103.13, 172.232, 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 96 16.00 O 3204 8.00 N 3048 7.00 C 14460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 187 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 187 " distance=2.03 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 198 " distance=2.03 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 192 " distance=2.03 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 187 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 192 " distance=2.03 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 187 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 198 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 192 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 187 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 198 " distance=2.03 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 192 " distance=2.03 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 187 " distance=2.03 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 198 " distance=2.03 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 192 " distance=2.03 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 187 " 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: 4.76 Conformation dependent library (CDL) restraints added in 2.2 seconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4440 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 68.4% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 4 through 14 removed outlier: 3.728A pdb=" N LYS A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 40 removed outlier: 4.107A pdb=" N SER A 27 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.763A pdb=" N ASP A 67 " --> pdb=" O ASN A 63 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 69 " --> pdb=" O CYS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 105 removed outlier: 3.746A pdb=" N PHE A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Proline residue: A 88 - end of helix removed outlier: 3.584A pdb=" N TYR A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 177 removed outlier: 3.562A pdb=" N ILE A 159 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 233 removed outlier: 3.690A pdb=" N PHE A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 217 " --> pdb=" O MET A 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 14 removed outlier: 3.728A pdb=" N LYS B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 40 removed outlier: 4.107A pdb=" N SER B 27 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR B 39 " --> pdb=" O LEU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.763A pdb=" N ASP B 67 " --> pdb=" O ASN B 63 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 69 " --> pdb=" O CYS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 105 removed outlier: 3.746A pdb=" N PHE B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Proline residue: B 88 - end of helix removed outlier: 3.583A pdb=" N TYR B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 177 removed outlier: 3.561A pdb=" N ILE B 159 " --> pdb=" O TYR B 155 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS B 162 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 233 removed outlier: 3.689A pdb=" N PHE B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 217 " --> pdb=" O MET B 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 14 removed outlier: 3.728A pdb=" N LYS C 9 " --> pdb=" O SER C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 40 removed outlier: 4.107A pdb=" N SER C 27 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR C 39 " --> pdb=" O LEU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.763A pdb=" N ASP C 67 " --> pdb=" O ASN C 63 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS C 68 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER C 69 " --> pdb=" O CYS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 105 removed outlier: 3.746A pdb=" N PHE C 84 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Proline residue: C 88 - end of helix removed outlier: 3.583A pdb=" N TYR C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 177 removed outlier: 3.561A pdb=" N ILE C 159 " --> pdb=" O TYR C 155 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS C 162 " --> pdb=" O SER C 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 172 " --> pdb=" O ALA C 168 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 233 removed outlier: 3.688A pdb=" N PHE C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 217 " --> pdb=" O MET C 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 14 removed outlier: 3.728A pdb=" N LYS D 9 " --> pdb=" O SER D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 40 removed outlier: 4.107A pdb=" N SER D 27 " --> pdb=" O LYS D 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL D 28 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR D 39 " --> pdb=" O LEU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.763A pdb=" N ASP D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS D 68 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER D 69 " --> pdb=" O CYS D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 105 removed outlier: 3.747A pdb=" N PHE D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Proline residue: D 88 - end of helix removed outlier: 3.583A pdb=" N TYR D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 177 removed outlier: 3.560A pdb=" N ILE D 159 " --> pdb=" O TYR D 155 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS D 162 " --> pdb=" O SER D 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE D 172 " --> pdb=" O ALA D 168 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 233 removed outlier: 3.688A pdb=" N PHE D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 217 " --> pdb=" O MET D 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU D 227 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 14 removed outlier: 3.728A pdb=" N LYS E 9 " --> pdb=" O SER E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 40 removed outlier: 4.108A pdb=" N SER E 27 " --> pdb=" O LYS E 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL E 28 " --> pdb=" O VAL E 24 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR E 39 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 70 removed outlier: 3.764A pdb=" N ASP E 67 " --> pdb=" O ASN E 63 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS E 68 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER E 69 " --> pdb=" O CYS E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 105 removed outlier: 3.746A pdb=" N PHE E 84 " --> pdb=" O LEU E 80 " (cutoff:3.500A) Proline residue: E 88 - end of helix removed outlier: 3.584A pdb=" N TYR E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 177 removed outlier: 3.561A pdb=" N ILE E 159 " --> pdb=" O TYR E 155 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE E 172 " --> pdb=" O ALA E 168 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN E 173 " --> pdb=" O PHE E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 233 removed outlier: 3.688A pdb=" N PHE E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER E 217 " --> pdb=" O MET E 213 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU E 227 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE E 232 " --> pdb=" O LEU E 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 14 removed outlier: 3.728A pdb=" N LYS F 9 " --> pdb=" O SER F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 40 removed outlier: 4.107A pdb=" N SER F 27 " --> pdb=" O LYS F 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL F 28 " --> pdb=" O VAL F 24 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR F 39 " --> pdb=" O LEU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 70 removed outlier: 3.763A pdb=" N ASP F 67 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS F 68 " --> pdb=" O VAL F 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER F 69 " --> pdb=" O CYS F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 105 removed outlier: 3.746A pdb=" N PHE F 84 " --> pdb=" O LEU F 80 " (cutoff:3.500A) Proline residue: F 88 - end of helix removed outlier: 3.583A pdb=" N TYR F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 177 removed outlier: 3.560A pdb=" N ILE F 159 " --> pdb=" O TYR F 155 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS F 162 " --> pdb=" O SER F 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE F 172 " --> pdb=" O ALA F 168 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN F 173 " --> pdb=" O PHE F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 233 removed outlier: 3.689A pdb=" N PHE F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER F 217 " --> pdb=" O MET F 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU F 227 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE F 232 " --> pdb=" O LEU F 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 14 removed outlier: 3.729A pdb=" N LYS G 9 " --> pdb=" O SER G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 40 removed outlier: 4.107A pdb=" N SER G 27 " --> pdb=" O LYS G 23 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL G 28 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR G 39 " --> pdb=" O LEU G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 70 removed outlier: 3.763A pdb=" N ASP G 67 " --> pdb=" O ASN G 63 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER G 69 " --> pdb=" O CYS G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 105 removed outlier: 3.746A pdb=" N PHE G 84 " --> pdb=" O LEU G 80 " (cutoff:3.500A) Proline residue: G 88 - end of helix removed outlier: 3.584A pdb=" N TYR G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 177 removed outlier: 3.562A pdb=" N ILE G 159 " --> pdb=" O TYR G 155 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS G 162 " --> pdb=" O SER G 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE G 172 " --> pdb=" O ALA G 168 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN G 173 " --> pdb=" O PHE G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 233 removed outlier: 3.689A pdb=" N PHE G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER G 217 " --> pdb=" O MET G 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU G 227 " --> pdb=" O LEU G 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE G 232 " --> pdb=" O LEU G 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 14 removed outlier: 3.728A pdb=" N LYS H 9 " --> pdb=" O SER H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 40 removed outlier: 4.107A pdb=" N SER H 27 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL H 28 " --> pdb=" O VAL H 24 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR H 39 " --> pdb=" O LEU H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 70 removed outlier: 3.763A pdb=" N ASP H 67 " --> pdb=" O ASN H 63 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS H 68 " --> pdb=" O VAL H 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER H 69 " --> pdb=" O CYS H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 105 removed outlier: 3.747A pdb=" N PHE H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Proline residue: H 88 - end of helix removed outlier: 3.584A pdb=" N TYR H 98 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 177 removed outlier: 3.500A pdb=" N TYR H 155 " --> pdb=" O LEU H 151 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE H 159 " --> pdb=" O TYR H 155 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS H 162 " --> pdb=" O SER H 158 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE H 172 " --> pdb=" O ALA H 168 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN H 173 " --> pdb=" O PHE H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 233 removed outlier: 3.690A pdb=" N PHE H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER H 217 " --> pdb=" O MET H 213 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU H 227 " --> pdb=" O LEU H 223 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE H 232 " --> pdb=" O LEU H 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 14 removed outlier: 3.728A pdb=" N LYS I 9 " --> pdb=" O SER I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 40 removed outlier: 4.107A pdb=" N SER I 27 " --> pdb=" O LYS I 23 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL I 28 " --> pdb=" O VAL I 24 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR I 39 " --> pdb=" O LEU I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 70 removed outlier: 3.763A pdb=" N ASP I 67 " --> pdb=" O ASN I 63 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS I 68 " --> pdb=" O VAL I 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER I 69 " --> pdb=" O CYS I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 105 removed outlier: 3.747A pdb=" N PHE I 84 " --> pdb=" O LEU I 80 " (cutoff:3.500A) Proline residue: I 88 - end of helix removed outlier: 3.584A pdb=" N TYR I 98 " --> pdb=" O ALA I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 177 removed outlier: 3.560A pdb=" N ILE I 159 " --> pdb=" O TYR I 155 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS I 162 " --> pdb=" O SER I 158 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE I 172 " --> pdb=" O ALA I 168 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN I 173 " --> pdb=" O PHE I 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 233 removed outlier: 3.688A pdb=" N PHE I 209 " --> pdb=" O GLU I 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER I 217 " --> pdb=" O MET I 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU I 227 " --> pdb=" O LEU I 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE I 232 " --> pdb=" O LEU I 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 14 removed outlier: 3.728A pdb=" N LYS J 9 " --> pdb=" O SER J 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 40 removed outlier: 4.107A pdb=" N SER J 27 " --> pdb=" O LYS J 23 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL J 28 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR J 39 " --> pdb=" O LEU J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 70 removed outlier: 3.764A pdb=" N ASP J 67 " --> pdb=" O ASN J 63 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS J 68 " --> pdb=" O VAL J 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER J 69 " --> pdb=" O CYS J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 105 removed outlier: 3.747A pdb=" N PHE J 84 " --> pdb=" O LEU J 80 " (cutoff:3.500A) Proline residue: J 88 - end of helix removed outlier: 3.584A pdb=" N TYR J 98 " --> pdb=" O ALA J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 177 removed outlier: 3.560A pdb=" N ILE J 159 " --> pdb=" O TYR J 155 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS J 162 " --> pdb=" O SER J 158 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE J 172 " --> pdb=" O ALA J 168 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN J 173 " --> pdb=" O PHE J 169 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 233 removed outlier: 3.689A pdb=" N PHE J 209 " --> pdb=" O GLU J 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER J 217 " --> pdb=" O MET J 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU J 227 " --> pdb=" O LEU J 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE J 232 " --> pdb=" O LEU J 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 14 removed outlier: 3.728A pdb=" N LYS K 9 " --> pdb=" O SER K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 40 removed outlier: 4.107A pdb=" N SER K 27 " --> pdb=" O LYS K 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL K 28 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR K 39 " --> pdb=" O LEU K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 70 removed outlier: 3.763A pdb=" N ASP K 67 " --> pdb=" O ASN K 63 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS K 68 " --> pdb=" O VAL K 64 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER K 69 " --> pdb=" O CYS K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 105 removed outlier: 3.747A pdb=" N PHE K 84 " --> pdb=" O LEU K 80 " (cutoff:3.500A) Proline residue: K 88 - end of helix removed outlier: 3.582A pdb=" N TYR K 98 " --> pdb=" O ALA K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 177 removed outlier: 3.561A pdb=" N ILE K 159 " --> pdb=" O TYR K 155 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS K 162 " --> pdb=" O SER K 158 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE K 172 " --> pdb=" O ALA K 168 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN K 173 " --> pdb=" O PHE K 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 233 removed outlier: 3.689A pdb=" N PHE K 209 " --> pdb=" O GLU K 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER K 217 " --> pdb=" O MET K 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU K 227 " --> pdb=" O LEU K 223 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE K 232 " --> pdb=" O LEU K 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 14 removed outlier: 3.728A pdb=" N LYS L 9 " --> pdb=" O SER L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 40 removed outlier: 4.108A pdb=" N SER L 27 " --> pdb=" O LYS L 23 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL L 28 " --> pdb=" O VAL L 24 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR L 39 " --> pdb=" O LEU L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 70 removed outlier: 3.763A pdb=" N ASP L 67 " --> pdb=" O ASN L 63 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS L 68 " --> pdb=" O VAL L 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER L 69 " --> pdb=" O CYS L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 105 removed outlier: 3.748A pdb=" N PHE L 84 " --> pdb=" O LEU L 80 " (cutoff:3.500A) Proline residue: L 88 - end of helix removed outlier: 3.583A pdb=" N TYR L 98 " --> pdb=" O ALA L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 177 removed outlier: 3.560A pdb=" N ILE L 159 " --> pdb=" O TYR L 155 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS L 162 " --> pdb=" O SER L 158 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE L 172 " --> pdb=" O ALA L 168 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN L 173 " --> pdb=" O PHE L 169 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 233 removed outlier: 3.688A pdb=" N PHE L 209 " --> pdb=" O GLU L 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER L 217 " --> pdb=" O MET L 213 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU L 227 " --> pdb=" O LEU L 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE L 232 " --> pdb=" O LEU L 228 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.659A pdb=" N ARG A 53 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.660A pdb=" N ARG B 53 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.660A pdb=" N ARG C 53 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.659A pdb=" N ARG D 53 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.660A pdb=" N ARG E 53 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.659A pdb=" N ARG F 53 " --> pdb=" O PHE F 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.659A pdb=" N ARG G 53 " --> pdb=" O PHE G 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.659A pdb=" N ARG H 53 " --> pdb=" O PHE H 199 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 53 through 54 removed outlier: 3.660A pdb=" N ARG I 53 " --> pdb=" O PHE I 199 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.660A pdb=" N ARG J 53 " --> pdb=" O PHE J 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.659A pdb=" N ARG K 53 " --> pdb=" O PHE K 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.659A pdb=" N ARG L 53 " --> pdb=" O PHE L 199 " (cutoff:3.500A) 1139 hydrogen bonds defined for protein. 3345 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: 5.45 Time building geometry restraints manager: 5.59 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: 5590 1.34 - 1.46: 4875 1.46 - 1.58: 10619 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 21204 Sorted by residual: bond pdb=" C VAL L 87 " pdb=" N PRO L 88 " ideal model delta sigma weight residual 1.336 1.360 -0.024 1.25e-02 6.40e+03 3.60e+00 bond pdb=" C VAL J 87 " pdb=" N PRO J 88 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.23e-02 6.61e+03 3.58e+00 bond pdb=" C VAL E 87 " pdb=" N PRO E 88 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.23e-02 6.61e+03 3.57e+00 bond pdb=" C VAL B 87 " pdb=" N PRO B 88 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.23e-02 6.61e+03 3.52e+00 bond pdb=" C VAL A 87 " pdb=" N PRO A 88 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.23e-02 6.61e+03 3.49e+00 ... (remaining 21199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 25835 2.25 - 4.51: 1874 4.51 - 6.76: 323 6.76 - 9.01: 12 9.01 - 11.27: 12 Bond angle restraints: 28056 Sorted by residual: angle pdb=" CA PRO D 88 " pdb=" N PRO D 88 " pdb=" CD PRO D 88 " ideal model delta sigma weight residual 112.00 107.10 4.90 1.40e+00 5.10e-01 1.22e+01 angle pdb=" CA PRO K 88 " pdb=" N PRO K 88 " pdb=" CD PRO K 88 " ideal model delta sigma weight residual 112.00 107.13 4.87 1.40e+00 5.10e-01 1.21e+01 angle pdb=" CA PRO A 88 " pdb=" N PRO A 88 " pdb=" CD PRO A 88 " ideal model delta sigma weight residual 112.00 107.13 4.87 1.40e+00 5.10e-01 1.21e+01 angle pdb=" CA PRO J 88 " pdb=" N PRO J 88 " pdb=" CD PRO J 88 " ideal model delta sigma weight residual 112.00 107.14 4.86 1.40e+00 5.10e-01 1.21e+01 angle pdb=" CA PRO H 88 " pdb=" N PRO H 88 " pdb=" CD PRO H 88 " ideal model delta sigma weight residual 112.00 107.14 4.86 1.40e+00 5.10e-01 1.20e+01 ... (remaining 28051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 10630 16.56 - 33.11: 1538 33.11 - 49.67: 492 49.67 - 66.22: 96 66.22 - 82.78: 36 Dihedral angle restraints: 12792 sinusoidal: 5916 harmonic: 6876 Sorted by residual: dihedral pdb=" C VAL K 87 " pdb=" N VAL K 87 " pdb=" CA VAL K 87 " pdb=" CB VAL K 87 " ideal model delta harmonic sigma weight residual -122.00 -130.32 8.32 0 2.50e+00 1.60e-01 1.11e+01 dihedral pdb=" C VAL E 87 " pdb=" N VAL E 87 " pdb=" CA VAL E 87 " pdb=" CB VAL E 87 " ideal model delta harmonic sigma weight residual -122.00 -130.31 8.31 0 2.50e+00 1.60e-01 1.10e+01 dihedral pdb=" C VAL F 87 " pdb=" N VAL F 87 " pdb=" CA VAL F 87 " pdb=" CB VAL F 87 " ideal model delta harmonic sigma weight residual -122.00 -130.28 8.28 0 2.50e+00 1.60e-01 1.10e+01 ... (remaining 12789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2168 0.049 - 0.099: 729 0.099 - 0.148: 103 0.148 - 0.198: 7 0.198 - 0.247: 17 Chirality restraints: 3024 Sorted by residual: chirality pdb=" CB VAL F 87 " pdb=" CA VAL F 87 " pdb=" CG1 VAL F 87 " pdb=" CG2 VAL F 87 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB VAL B 87 " pdb=" CA VAL B 87 " pdb=" CG1 VAL B 87 " pdb=" CG2 VAL B 87 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB VAL C 87 " pdb=" CA VAL C 87 " pdb=" CG1 VAL C 87 " pdb=" CG2 VAL C 87 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 3021 not shown) Planarity restraints: 3204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS H 192 " 0.034 5.00e-02 4.00e+02 5.05e-02 4.08e+00 pdb=" N PRO H 193 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO H 193 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 193 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS F 192 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.04e+00 pdb=" N PRO F 193 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO F 193 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 193 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 192 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.02e+00 pdb=" N PRO A 193 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 193 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 193 " -0.028 5.00e-02 4.00e+02 ... (remaining 3201 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6206 2.81 - 3.34: 16621 3.34 - 3.86: 31105 3.86 - 4.38: 34287 4.38 - 4.90: 60986 Nonbonded interactions: 149205 Sorted by model distance: nonbonded pdb=" O PRO A 203 " pdb=" OG1 THR A 207 " model vdw 2.293 3.040 nonbonded pdb=" O PRO G 203 " pdb=" OG1 THR G 207 " model vdw 2.293 3.040 nonbonded pdb=" O PRO F 203 " pdb=" OG1 THR F 207 " model vdw 2.293 3.040 nonbonded pdb=" O PRO K 203 " pdb=" OG1 THR K 207 " model vdw 2.293 3.040 nonbonded pdb=" O PRO C 203 " pdb=" OG1 THR C 207 " model vdw 2.293 3.040 ... (remaining 149200 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 2 through 235 or resid 401 through 409)) selection = (chain 'B' and (resid 2 through 235 or resid 401 through 409)) selection = (chain 'C' and (resid 2 through 235 or resid 401 through 409)) selection = (chain 'D' and (resid 2 through 235 or resid 401 through 409)) selection = chain 'E' selection = (chain 'F' and (resid 2 through 235 or resid 401 through 409)) selection = (chain 'G' and (resid 2 through 235 or resid 401 through 409)) selection = (chain 'H' and (resid 2 through 235 or resid 401 through 409)) selection = (chain 'I' and (resid 2 through 235 or resid 401 through 409)) selection = (chain 'J' and (resid 2 through 235 or resid 401 through 409)) selection = chain 'K' selection = (chain 'L' and (resid 2 through 235 or resid 401 through 409)) } 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 group one per residue 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: 17.720 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: 0.040 Extract box with map and model: 1.110 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 45.500 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 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 : 0.007 0.051 21204 Z= 0.463 Angle : 1.261 11.268 28056 Z= 0.576 Chirality : 0.050 0.247 3024 Planarity : 0.006 0.051 3204 Dihedral : 16.993 82.776 8244 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.00 % Allowed : 10.29 % Favored : 85.71 % 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: -5.48 (0.11), residues: 2304 helix: -3.98 (0.05), residues: 1548 sheet: 1.37 (0.48), residues: 132 loop : -3.13 (0.20), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 45 HIS 0.004 0.001 HIS H 95 PHE 0.020 0.002 PHE F 52 TYR 0.008 0.002 TYR A 155 ARG 0.002 0.000 ARG K 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 552 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7816 (t0) cc_final: 0.7502 (t70) REVERT: A 47 ASP cc_start: 0.9174 (p0) cc_final: 0.8857 (p0) REVERT: A 82 ILE cc_start: 0.8793 (tt) cc_final: 0.8593 (tp) REVERT: A 185 TYR cc_start: 0.9025 (t80) cc_final: 0.8666 (t80) REVERT: A 213 MET cc_start: 0.8445 (mmm) cc_final: 0.7182 (mmm) REVERT: B 3 ASP cc_start: 0.7643 (t0) cc_final: 0.7186 (t70) REVERT: B 42 GLU cc_start: 0.7786 (tp30) cc_final: 0.7579 (tp30) REVERT: B 55 ASN cc_start: 0.9229 (t0) cc_final: 0.8792 (t0) REVERT: B 206 LYS cc_start: 0.9157 (mttt) cc_final: 0.8490 (mttp) REVERT: C 55 ASN cc_start: 0.9171 (t0) cc_final: 0.8957 (t0) REVERT: D 3 ASP cc_start: 0.7910 (t0) cc_final: 0.7571 (t70) REVERT: D 42 GLU cc_start: 0.7924 (tp30) cc_final: 0.7612 (tp30) REVERT: D 47 ASP cc_start: 0.9156 (p0) cc_final: 0.8767 (p0) REVERT: D 185 TYR cc_start: 0.9027 (t80) cc_final: 0.8677 (t80) REVERT: D 213 MET cc_start: 0.8437 (mmm) cc_final: 0.7134 (mmm) REVERT: E 3 ASP cc_start: 0.7933 (t0) cc_final: 0.7444 (t70) REVERT: E 47 ASP cc_start: 0.8919 (p0) cc_final: 0.8542 (p0) REVERT: E 185 TYR cc_start: 0.9033 (t80) cc_final: 0.8546 (t80) REVERT: F 3 ASP cc_start: 0.7997 (t0) cc_final: 0.7537 (t70) REVERT: F 55 ASN cc_start: 0.9145 (t0) cc_final: 0.8797 (t0) REVERT: G 3 ASP cc_start: 0.7458 (t0) cc_final: 0.7063 (t70) REVERT: G 47 ASP cc_start: 0.9129 (p0) cc_final: 0.8893 (p0) REVERT: G 53 ARG cc_start: 0.8290 (mtt90) cc_final: 0.8046 (mtt90) REVERT: G 55 ASN cc_start: 0.9159 (t0) cc_final: 0.8915 (t0) REVERT: H 3 ASP cc_start: 0.7598 (t0) cc_final: 0.7286 (t70) REVERT: H 47 ASP cc_start: 0.9167 (p0) cc_final: 0.8830 (p0) REVERT: H 55 ASN cc_start: 0.9288 (t0) cc_final: 0.8934 (t0) REVERT: H 82 ILE cc_start: 0.8755 (tt) cc_final: 0.8515 (tp) REVERT: H 98 TYR cc_start: 0.8748 (m-80) cc_final: 0.8450 (m-80) REVERT: I 3 ASP cc_start: 0.7672 (t0) cc_final: 0.7070 (t70) REVERT: I 98 TYR cc_start: 0.8740 (m-80) cc_final: 0.8478 (m-10) REVERT: I 206 LYS cc_start: 0.9088 (mttt) cc_final: 0.8452 (mttp) REVERT: J 3 ASP cc_start: 0.7983 (t0) cc_final: 0.7597 (t70) REVERT: J 55 ASN cc_start: 0.9155 (t0) cc_final: 0.8824 (t0) REVERT: K 3 ASP cc_start: 0.7936 (t0) cc_final: 0.7514 (t70) REVERT: K 47 ASP cc_start: 0.9072 (p0) cc_final: 0.8716 (p0) REVERT: K 82 ILE cc_start: 0.8806 (tt) cc_final: 0.8590 (tp) REVERT: K 104 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8410 (mt-10) REVERT: K 185 TYR cc_start: 0.9049 (t80) cc_final: 0.8577 (t80) REVERT: K 213 MET cc_start: 0.8397 (mmm) cc_final: 0.7037 (mmm) REVERT: L 3 ASP cc_start: 0.7685 (t0) cc_final: 0.7173 (t70) REVERT: L 55 ASN cc_start: 0.9257 (t0) cc_final: 0.8844 (t0) REVERT: L 206 LYS cc_start: 0.9150 (mttt) cc_final: 0.8474 (mttp) REVERT: L 224 ASN cc_start: 0.9087 (m-40) cc_final: 0.8876 (m110) outliers start: 84 outliers final: 43 residues processed: 609 average time/residue: 0.3385 time to fit residues: 307.1069 Evaluate side-chains 519 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 476 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 5 SER Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain H residue 5 SER Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain J residue 5 SER Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain L residue 5 SER Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 226 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.8980 chunk 172 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 224 ASN B 49 GLN B 58 GLN B 81 GLN C 49 GLN C 58 GLN C 81 GLN D 49 GLN D 224 ASN E 49 GLN F 49 GLN F 58 GLN F 81 GLN F 224 ASN G 49 GLN G 58 GLN H 49 GLN I 49 GLN I 58 GLN I 81 GLN J 49 GLN J 81 GLN J 224 ASN K 49 GLN K 224 ASN L 49 GLN L 58 GLN L 81 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21204 Z= 0.166 Angle : 0.577 8.817 28056 Z= 0.290 Chirality : 0.038 0.187 3024 Planarity : 0.005 0.036 3204 Dihedral : 10.346 58.152 3903 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.29 % Allowed : 16.48 % Favored : 80.24 % 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: -2.10 (0.15), residues: 2304 helix: -0.94 (0.11), residues: 1572 sheet: 1.58 (0.48), residues: 132 loop : -3.02 (0.20), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 45 HIS 0.002 0.001 HIS D 95 PHE 0.017 0.001 PHE H 30 TYR 0.020 0.001 TYR D 230 ARG 0.004 0.000 ARG F 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 550 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7603 (t0) cc_final: 0.7270 (t70) REVERT: A 42 GLU cc_start: 0.7877 (tp30) cc_final: 0.7611 (tp30) REVERT: A 47 ASP cc_start: 0.9164 (p0) cc_final: 0.8881 (p0) REVERT: A 55 ASN cc_start: 0.9119 (t0) cc_final: 0.8641 (t0) REVERT: B 3 ASP cc_start: 0.7498 (t0) cc_final: 0.6688 (t70) REVERT: B 55 ASN cc_start: 0.9105 (t0) cc_final: 0.8686 (t0) REVERT: B 213 MET cc_start: 0.8365 (mmm) cc_final: 0.6885 (mmm) REVERT: C 55 ASN cc_start: 0.9009 (t0) cc_final: 0.8623 (t0) REVERT: C 152 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8721 (mt) REVERT: C 153 ARG cc_start: 0.7562 (tpt170) cc_final: 0.7341 (mmm160) REVERT: D 3 ASP cc_start: 0.7790 (t0) cc_final: 0.7244 (t70) REVERT: D 47 ASP cc_start: 0.9106 (p0) cc_final: 0.8680 (p0) REVERT: D 55 ASN cc_start: 0.9140 (t0) cc_final: 0.8842 (t0) REVERT: E 47 ASP cc_start: 0.9084 (p0) cc_final: 0.8776 (p0) REVERT: E 55 ASN cc_start: 0.9181 (t0) cc_final: 0.8834 (t0) REVERT: E 213 MET cc_start: 0.8341 (mmm) cc_final: 0.7138 (mmm) REVERT: F 3 ASP cc_start: 0.7828 (t0) cc_final: 0.7119 (t70) REVERT: F 55 ASN cc_start: 0.9090 (t0) cc_final: 0.8788 (t0) REVERT: F 76 ARG cc_start: 0.8832 (mtt90) cc_final: 0.8601 (mtt90) REVERT: G 3 ASP cc_start: 0.7271 (t0) cc_final: 0.6723 (t70) REVERT: G 47 ASP cc_start: 0.9111 (p0) cc_final: 0.8900 (p0) REVERT: G 55 ASN cc_start: 0.9103 (t0) cc_final: 0.8810 (t0) REVERT: H 3 ASP cc_start: 0.7469 (t0) cc_final: 0.6779 (t70) REVERT: H 47 ASP cc_start: 0.9171 (p0) cc_final: 0.8909 (p0) REVERT: H 55 ASN cc_start: 0.9132 (t0) cc_final: 0.8811 (t0) REVERT: I 47 ASP cc_start: 0.8917 (p0) cc_final: 0.8687 (p0) REVERT: I 55 ASN cc_start: 0.9108 (t0) cc_final: 0.8747 (t0) REVERT: J 3 ASP cc_start: 0.7833 (t0) cc_final: 0.7389 (t70) REVERT: J 55 ASN cc_start: 0.9095 (t0) cc_final: 0.8757 (t0) REVERT: K 3 ASP cc_start: 0.7810 (t0) cc_final: 0.7200 (t70) REVERT: K 47 ASP cc_start: 0.9072 (p0) cc_final: 0.8673 (p0) REVERT: K 55 ASN cc_start: 0.9153 (t0) cc_final: 0.8706 (t0) REVERT: L 3 ASP cc_start: 0.7566 (t0) cc_final: 0.6674 (t70) REVERT: L 55 ASN cc_start: 0.9116 (t0) cc_final: 0.8706 (t0) REVERT: L 76 ARG cc_start: 0.8943 (mtt90) cc_final: 0.8557 (mtt90) REVERT: L 213 MET cc_start: 0.8350 (mmm) cc_final: 0.6864 (mmm) outliers start: 69 outliers final: 48 residues processed: 577 average time/residue: 0.3236 time to fit residues: 286.2821 Evaluate side-chains 547 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 498 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 5 SER Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 5 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain J residue 5 SER Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 63 ASN Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 232 PHE Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 5 SER Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 89 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 224 optimal weight: 0.7980 chunk 184 optimal weight: 9.9990 chunk 205 optimal weight: 0.3980 chunk 70 optimal weight: 4.9990 chunk 166 optimal weight: 0.5980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 63 ASN B 63 ASN B 81 GLN C 63 ASN C 81 GLN D 81 GLN E 58 GLN E 81 GLN F 63 ASN F 81 GLN G 63 ASN G 81 GLN H 58 GLN H 63 ASN I 81 GLN J 58 GLN J 63 ASN J 81 GLN L 81 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21204 Z= 0.138 Angle : 0.533 8.601 28056 Z= 0.264 Chirality : 0.037 0.154 3024 Planarity : 0.004 0.032 3204 Dihedral : 9.110 58.108 3876 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.71 % Allowed : 19.76 % Favored : 77.52 % 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: -0.31 (0.17), residues: 2304 helix: 0.51 (0.13), residues: 1584 sheet: 1.63 (0.48), residues: 132 loop : -2.56 (0.22), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 45 HIS 0.001 0.000 HIS J 194 PHE 0.018 0.001 PHE C 30 TYR 0.016 0.001 TYR B 92 ARG 0.004 0.000 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 541 time to evaluate : 2.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7520 (t0) cc_final: 0.7179 (t70) REVERT: A 47 ASP cc_start: 0.9089 (p0) cc_final: 0.8621 (p0) REVERT: A 55 ASN cc_start: 0.9076 (t0) cc_final: 0.8631 (t0) REVERT: B 3 ASP cc_start: 0.7419 (t0) cc_final: 0.6613 (t70) REVERT: B 47 ASP cc_start: 0.9062 (p0) cc_final: 0.8780 (p0) REVERT: B 55 ASN cc_start: 0.9048 (t0) cc_final: 0.8635 (t0) REVERT: C 55 ASN cc_start: 0.8988 (t0) cc_final: 0.8661 (t0) REVERT: C 152 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8725 (mt) REVERT: C 153 ARG cc_start: 0.7587 (tpt170) cc_final: 0.7304 (mmm160) REVERT: D 3 ASP cc_start: 0.7714 (t0) cc_final: 0.7157 (t70) REVERT: D 47 ASP cc_start: 0.8992 (p0) cc_final: 0.8570 (p0) REVERT: D 55 ASN cc_start: 0.9098 (t0) cc_final: 0.8854 (t0) REVERT: D 76 ARG cc_start: 0.8603 (mtt90) cc_final: 0.8346 (mtt90) REVERT: E 47 ASP cc_start: 0.9069 (p0) cc_final: 0.8740 (p0) REVERT: E 55 ASN cc_start: 0.9105 (t0) cc_final: 0.8707 (t0) REVERT: E 152 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8761 (mt) REVERT: E 213 MET cc_start: 0.8354 (mmm) cc_final: 0.7032 (mmm) REVERT: F 3 ASP cc_start: 0.7756 (t0) cc_final: 0.7073 (t70) REVERT: F 55 ASN cc_start: 0.9037 (t0) cc_final: 0.8533 (t0) REVERT: F 103 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8094 (mp0) REVERT: F 166 GLU cc_start: 0.8580 (tp30) cc_final: 0.8322 (tp30) REVERT: F 213 MET cc_start: 0.8530 (mmm) cc_final: 0.7549 (mmm) REVERT: G 3 ASP cc_start: 0.7187 (t0) cc_final: 0.6629 (t70) REVERT: G 47 ASP cc_start: 0.9076 (p0) cc_final: 0.8733 (p0) REVERT: G 55 ASN cc_start: 0.9060 (t0) cc_final: 0.8816 (t0) REVERT: H 3 ASP cc_start: 0.7403 (t0) cc_final: 0.6704 (t70) REVERT: H 47 ASP cc_start: 0.9101 (p0) cc_final: 0.8828 (p0) REVERT: H 55 ASN cc_start: 0.9092 (t0) cc_final: 0.8828 (t0) REVERT: I 47 ASP cc_start: 0.8899 (p0) cc_final: 0.8444 (p0) REVERT: I 55 ASN cc_start: 0.9049 (t0) cc_final: 0.8677 (t0) REVERT: I 152 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8739 (mt) REVERT: J 3 ASP cc_start: 0.7742 (t0) cc_final: 0.7294 (t70) REVERT: J 55 ASN cc_start: 0.9084 (t0) cc_final: 0.8811 (t0) REVERT: J 213 MET cc_start: 0.8516 (mmm) cc_final: 0.7506 (mmm) REVERT: K 3 ASP cc_start: 0.7679 (t0) cc_final: 0.7066 (t70) REVERT: K 47 ASP cc_start: 0.8950 (p0) cc_final: 0.8525 (p0) REVERT: K 55 ASN cc_start: 0.9106 (t0) cc_final: 0.8663 (t0) REVERT: L 3 ASP cc_start: 0.7464 (t0) cc_final: 0.6597 (t70) REVERT: L 55 ASN cc_start: 0.9079 (t0) cc_final: 0.8692 (t0) outliers start: 57 outliers final: 41 residues processed: 560 average time/residue: 0.3436 time to fit residues: 290.9908 Evaluate side-chains 538 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 494 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 232 PHE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 63 ASN Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 232 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 220 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN C 81 GLN D 58 GLN E 81 GLN F 63 ASN F 81 GLN G 81 GLN I 81 GLN J 63 ASN J 81 GLN K 58 GLN L 63 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21204 Z= 0.232 Angle : 0.563 7.552 28056 Z= 0.284 Chirality : 0.039 0.138 3024 Planarity : 0.004 0.032 3204 Dihedral : 9.425 57.929 3864 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.33 % Allowed : 20.24 % Favored : 75.43 % 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: 0.44 (0.18), residues: 2304 helix: 1.13 (0.13), residues: 1584 sheet: 1.59 (0.48), residues: 132 loop : -2.37 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 174 HIS 0.002 0.001 HIS B 74 PHE 0.028 0.001 PHE C 30 TYR 0.023 0.001 TYR F 230 ARG 0.003 0.000 ARG L 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 516 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7527 (t0) cc_final: 0.6921 (t70) REVERT: A 47 ASP cc_start: 0.9029 (p0) cc_final: 0.8737 (p0) REVERT: A 55 ASN cc_start: 0.9151 (t0) cc_final: 0.8696 (t0) REVERT: B 3 ASP cc_start: 0.7447 (t0) cc_final: 0.6687 (t70) REVERT: B 55 ASN cc_start: 0.9129 (t0) cc_final: 0.8753 (t0) REVERT: B 152 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8818 (mt) REVERT: C 3 ASP cc_start: 0.7552 (t0) cc_final: 0.6762 (t70) REVERT: C 42 GLU cc_start: 0.7752 (tp30) cc_final: 0.7483 (tp30) REVERT: C 47 ASP cc_start: 0.8992 (p0) cc_final: 0.8694 (p0) REVERT: C 55 ASN cc_start: 0.9095 (t0) cc_final: 0.8824 (t0) REVERT: C 152 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8754 (mt) REVERT: D 3 ASP cc_start: 0.7666 (t0) cc_final: 0.7105 (t70) REVERT: D 47 ASP cc_start: 0.9047 (p0) cc_final: 0.8640 (p0) REVERT: D 55 ASN cc_start: 0.9143 (t0) cc_final: 0.8669 (t0) REVERT: D 213 MET cc_start: 0.8466 (mmm) cc_final: 0.7691 (mmm) REVERT: E 3 ASP cc_start: 0.7722 (t0) cc_final: 0.7328 (t70) REVERT: E 47 ASP cc_start: 0.9094 (p0) cc_final: 0.8737 (p0) REVERT: E 55 ASN cc_start: 0.9118 (t0) cc_final: 0.8766 (t0) REVERT: E 152 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8798 (mt) REVERT: E 213 MET cc_start: 0.8427 (mmm) cc_final: 0.7187 (mmm) REVERT: F 3 ASP cc_start: 0.7667 (t0) cc_final: 0.7084 (t70) REVERT: F 47 ASP cc_start: 0.8996 (p0) cc_final: 0.8735 (p0) REVERT: F 55 ASN cc_start: 0.9104 (t0) cc_final: 0.8853 (t0) REVERT: F 76 ARG cc_start: 0.8995 (mtt90) cc_final: 0.8537 (mtt90) REVERT: F 166 GLU cc_start: 0.8616 (tp30) cc_final: 0.8356 (tp30) REVERT: G 3 ASP cc_start: 0.7288 (t0) cc_final: 0.6714 (t70) REVERT: G 42 GLU cc_start: 0.7630 (tp30) cc_final: 0.7321 (tp30) REVERT: G 55 ASN cc_start: 0.9118 (t0) cc_final: 0.8892 (t0) REVERT: H 3 ASP cc_start: 0.7431 (t0) cc_final: 0.6769 (t70) REVERT: H 42 GLU cc_start: 0.7628 (tp30) cc_final: 0.7322 (tp30) REVERT: H 47 ASP cc_start: 0.9018 (p0) cc_final: 0.8747 (p0) REVERT: H 55 ASN cc_start: 0.9155 (t0) cc_final: 0.8694 (t0) REVERT: I 3 ASP cc_start: 0.7608 (t0) cc_final: 0.7109 (t70) REVERT: I 42 GLU cc_start: 0.7893 (tp30) cc_final: 0.7665 (tp30) REVERT: I 47 ASP cc_start: 0.8940 (p0) cc_final: 0.8441 (p0) REVERT: I 55 ASN cc_start: 0.9113 (t0) cc_final: 0.8787 (t0) REVERT: I 152 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8759 (mt) REVERT: J 3 ASP cc_start: 0.7658 (t0) cc_final: 0.7188 (t70) REVERT: J 47 ASP cc_start: 0.9014 (p0) cc_final: 0.8731 (p0) REVERT: J 55 ASN cc_start: 0.9138 (t0) cc_final: 0.8896 (t0) REVERT: K 3 ASP cc_start: 0.7627 (t0) cc_final: 0.7068 (t70) REVERT: K 47 ASP cc_start: 0.8961 (p0) cc_final: 0.8553 (p0) REVERT: K 55 ASN cc_start: 0.9176 (t0) cc_final: 0.8728 (t0) REVERT: L 3 ASP cc_start: 0.7543 (t0) cc_final: 0.6711 (t70) REVERT: L 55 ASN cc_start: 0.9144 (t0) cc_final: 0.8761 (t0) REVERT: L 152 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8826 (mt) outliers start: 91 outliers final: 51 residues processed: 551 average time/residue: 0.3065 time to fit residues: 259.0184 Evaluate side-chains 552 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 496 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 224 ASN Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 224 ASN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 152 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 164 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 188 optimal weight: 0.7980 chunk 152 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 chunk 197 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN C 81 GLN D 63 ASN E 63 ASN E 81 GLN F 81 GLN G 81 GLN I 63 ASN I 81 GLN J 81 GLN K 63 ASN L 81 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21204 Z= 0.143 Angle : 0.516 8.786 28056 Z= 0.256 Chirality : 0.037 0.119 3024 Planarity : 0.003 0.029 3204 Dihedral : 8.741 59.558 3864 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.62 % Allowed : 23.00 % Favored : 74.38 % 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: 1.04 (0.18), residues: 2304 helix: 1.59 (0.13), residues: 1560 sheet: 1.60 (0.48), residues: 132 loop : -1.96 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 45 HIS 0.001 0.000 HIS J 95 PHE 0.017 0.001 PHE C 30 TYR 0.017 0.001 TYR H 230 ARG 0.002 0.000 ARG I 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 541 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7416 (t0) cc_final: 0.6780 (t70) REVERT: A 47 ASP cc_start: 0.8980 (p0) cc_final: 0.8517 (p0) REVERT: A 55 ASN cc_start: 0.9035 (t0) cc_final: 0.8519 (t0) REVERT: A 213 MET cc_start: 0.8556 (mmm) cc_final: 0.7782 (mmm) REVERT: B 3 ASP cc_start: 0.7391 (t0) cc_final: 0.6596 (t70) REVERT: B 55 ASN cc_start: 0.9039 (t0) cc_final: 0.8677 (t0) REVERT: B 103 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8577 (mp0) REVERT: B 152 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8776 (mt) REVERT: B 218 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8695 (mm) REVERT: C 42 GLU cc_start: 0.7722 (tp30) cc_final: 0.7479 (tp30) REVERT: C 47 ASP cc_start: 0.8939 (p0) cc_final: 0.8518 (p0) REVERT: C 55 ASN cc_start: 0.9002 (t0) cc_final: 0.8721 (t0) REVERT: C 103 GLU cc_start: 0.8946 (mt-10) cc_final: 0.7993 (mp0) REVERT: C 152 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8652 (mt) REVERT: C 162 LYS cc_start: 0.7486 (mtpt) cc_final: 0.7267 (mtpp) REVERT: D 3 ASP cc_start: 0.7568 (t0) cc_final: 0.6985 (t70) REVERT: D 47 ASP cc_start: 0.8965 (p0) cc_final: 0.8357 (p0) REVERT: D 55 ASN cc_start: 0.9047 (t0) cc_final: 0.8576 (t0) REVERT: E 47 ASP cc_start: 0.9094 (p0) cc_final: 0.8729 (p0) REVERT: E 55 ASN cc_start: 0.9016 (t0) cc_final: 0.8668 (t0) REVERT: E 152 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8757 (mt) REVERT: F 3 ASP cc_start: 0.7555 (t0) cc_final: 0.6825 (t70) REVERT: F 47 ASP cc_start: 0.8974 (p0) cc_final: 0.8545 (p0) REVERT: F 55 ASN cc_start: 0.9010 (t0) cc_final: 0.8772 (t0) REVERT: F 76 ARG cc_start: 0.8862 (mtt90) cc_final: 0.8481 (mtt90) REVERT: F 152 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8640 (mt) REVERT: F 161 PHE cc_start: 0.8782 (m-80) cc_final: 0.8561 (m-80) REVERT: F 166 GLU cc_start: 0.8591 (tp30) cc_final: 0.8342 (tp30) REVERT: F 213 MET cc_start: 0.8400 (mmm) cc_final: 0.7240 (mmm) REVERT: G 3 ASP cc_start: 0.7302 (t0) cc_final: 0.6667 (t70) REVERT: G 47 ASP cc_start: 0.8922 (p0) cc_final: 0.8448 (p0) REVERT: G 55 ASN cc_start: 0.9045 (t0) cc_final: 0.8819 (t0) REVERT: G 200 LEU cc_start: 0.8986 (mp) cc_final: 0.8758 (mt) REVERT: H 3 ASP cc_start: 0.7354 (t0) cc_final: 0.6732 (t70) REVERT: H 47 ASP cc_start: 0.8966 (p0) cc_final: 0.8491 (p0) REVERT: H 55 ASN cc_start: 0.9062 (t0) cc_final: 0.8587 (t0) REVERT: H 105 LYS cc_start: 0.9157 (ptmt) cc_final: 0.8951 (ptmt) REVERT: I 42 GLU cc_start: 0.7835 (tp30) cc_final: 0.7615 (tp30) REVERT: I 55 ASN cc_start: 0.9046 (t0) cc_final: 0.8722 (t0) REVERT: I 152 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8740 (mt) REVERT: J 3 ASP cc_start: 0.7570 (t0) cc_final: 0.6860 (t70) REVERT: J 47 ASP cc_start: 0.8980 (p0) cc_final: 0.8552 (p0) REVERT: J 55 ASN cc_start: 0.9051 (t0) cc_final: 0.8820 (t0) REVERT: J 76 ARG cc_start: 0.8854 (mtt90) cc_final: 0.8490 (mtt90) REVERT: J 152 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8619 (mt) REVERT: J 161 PHE cc_start: 0.8813 (m-80) cc_final: 0.8558 (m-80) REVERT: J 166 GLU cc_start: 0.8597 (tp30) cc_final: 0.8355 (tp30) REVERT: J 213 MET cc_start: 0.8404 (mmm) cc_final: 0.7248 (mmm) REVERT: K 3 ASP cc_start: 0.7531 (t0) cc_final: 0.6924 (t70) REVERT: K 47 ASP cc_start: 0.8895 (p0) cc_final: 0.8440 (p0) REVERT: K 55 ASN cc_start: 0.9067 (t0) cc_final: 0.8549 (t0) REVERT: K 213 MET cc_start: 0.8461 (mmm) cc_final: 0.7404 (mmm) REVERT: L 3 ASP cc_start: 0.7452 (t0) cc_final: 0.6603 (t70) REVERT: L 55 ASN cc_start: 0.9054 (t0) cc_final: 0.8679 (t0) REVERT: L 152 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8781 (mt) REVERT: L 213 MET cc_start: 0.8454 (mmm) cc_final: 0.7576 (mmm) REVERT: L 218 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8694 (mm) outliers start: 55 outliers final: 30 residues processed: 557 average time/residue: 0.3191 time to fit residues: 271.0355 Evaluate side-chains 547 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 508 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 12 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 232 PHE Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 232 PHE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 232 PHE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 232 PHE Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain L residue 218 LEU Chi-restraints excluded: chain L residue 232 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.9990 chunk 198 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 129 optimal weight: 0.0040 chunk 54 optimal weight: 2.9990 chunk 220 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 72 optimal weight: 20.0000 chunk 115 optimal weight: 0.3980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN B 81 GLN E 81 GLN F 63 ASN F 81 GLN G 81 GLN J 81 GLN K 81 GLN L 224 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21204 Z= 0.129 Angle : 0.514 9.064 28056 Z= 0.254 Chirality : 0.037 0.112 3024 Planarity : 0.003 0.029 3204 Dihedral : 8.244 59.923 3852 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.57 % Allowed : 23.14 % Favored : 74.29 % 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: 1.35 (0.18), residues: 2304 helix: 1.83 (0.13), residues: 1560 sheet: 1.67 (0.48), residues: 132 loop : -1.83 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP F 25 HIS 0.002 0.000 HIS J 95 PHE 0.015 0.001 PHE C 30 TYR 0.018 0.001 TYR L 230 ARG 0.002 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 563 time to evaluate : 2.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7392 (t0) cc_final: 0.6751 (t70) REVERT: A 47 ASP cc_start: 0.8939 (p0) cc_final: 0.8249 (p0) REVERT: A 55 ASN cc_start: 0.8986 (t0) cc_final: 0.8462 (t0) REVERT: A 223 LEU cc_start: 0.8745 (mt) cc_final: 0.8438 (mt) REVERT: B 3 ASP cc_start: 0.7370 (t0) cc_final: 0.6582 (t70) REVERT: B 47 ASP cc_start: 0.8985 (p0) cc_final: 0.8508 (p0) REVERT: B 55 ASN cc_start: 0.9005 (t0) cc_final: 0.8649 (t0) REVERT: B 152 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8774 (mt) REVERT: B 213 MET cc_start: 0.8446 (mmm) cc_final: 0.7648 (mmm) REVERT: C 3 ASP cc_start: 0.7453 (t0) cc_final: 0.6749 (t70) REVERT: C 42 GLU cc_start: 0.7721 (tp30) cc_final: 0.7512 (tp30) REVERT: C 47 ASP cc_start: 0.8880 (p0) cc_final: 0.8221 (p0) REVERT: C 55 ASN cc_start: 0.8969 (t0) cc_final: 0.8707 (t0) REVERT: C 103 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8685 (mm-30) REVERT: C 152 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8737 (mt) REVERT: C 162 LYS cc_start: 0.7420 (mtpt) cc_final: 0.7168 (mtpp) REVERT: D 3 ASP cc_start: 0.7543 (t0) cc_final: 0.6927 (t70) REVERT: D 47 ASP cc_start: 0.8914 (p0) cc_final: 0.8383 (p0) REVERT: D 55 ASN cc_start: 0.8988 (t0) cc_final: 0.8482 (t0) REVERT: D 213 MET cc_start: 0.8509 (mmm) cc_final: 0.7460 (mmm) REVERT: D 223 LEU cc_start: 0.8739 (mt) cc_final: 0.8421 (mt) REVERT: E 3 ASP cc_start: 0.7586 (t0) cc_final: 0.6890 (t70) REVERT: E 47 ASP cc_start: 0.9081 (p0) cc_final: 0.8691 (p0) REVERT: E 55 ASN cc_start: 0.8977 (t0) cc_final: 0.8643 (t0) REVERT: E 152 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8743 (mt) REVERT: F 3 ASP cc_start: 0.7549 (t0) cc_final: 0.6789 (t70) REVERT: F 47 ASP cc_start: 0.8936 (p0) cc_final: 0.8263 (p0) REVERT: F 55 ASN cc_start: 0.8991 (t0) cc_final: 0.8759 (t0) REVERT: F 103 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8228 (mp0) REVERT: F 152 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8690 (mt) REVERT: F 166 GLU cc_start: 0.8563 (tp30) cc_final: 0.8290 (tp30) REVERT: G 3 ASP cc_start: 0.7285 (t0) cc_final: 0.6641 (t70) REVERT: G 47 ASP cc_start: 0.8862 (p0) cc_final: 0.8182 (p0) REVERT: G 55 ASN cc_start: 0.8999 (t0) cc_final: 0.8790 (t0) REVERT: G 213 MET cc_start: 0.8392 (mmm) cc_final: 0.7597 (mmm) REVERT: H 3 ASP cc_start: 0.7349 (t0) cc_final: 0.6734 (t70) REVERT: H 47 ASP cc_start: 0.8930 (p0) cc_final: 0.8254 (p0) REVERT: H 55 ASN cc_start: 0.9013 (t0) cc_final: 0.8489 (t0) REVERT: I 3 ASP cc_start: 0.7509 (t0) cc_final: 0.6699 (t70) REVERT: I 55 ASN cc_start: 0.9008 (t0) cc_final: 0.8672 (t0) REVERT: I 152 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8733 (mt) REVERT: I 162 LYS cc_start: 0.7398 (mtpt) cc_final: 0.7132 (mtpp) REVERT: J 3 ASP cc_start: 0.7559 (t0) cc_final: 0.6823 (t70) REVERT: J 47 ASP cc_start: 0.8932 (p0) cc_final: 0.8279 (p0) REVERT: J 55 ASN cc_start: 0.9034 (t0) cc_final: 0.8797 (t0) REVERT: J 152 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8675 (mt) REVERT: J 166 GLU cc_start: 0.8597 (tp30) cc_final: 0.8347 (tp30) REVERT: K 3 ASP cc_start: 0.7505 (t0) cc_final: 0.6891 (t70) REVERT: K 47 ASP cc_start: 0.8848 (p0) cc_final: 0.8275 (p0) REVERT: K 55 ASN cc_start: 0.9024 (t0) cc_final: 0.8491 (t0) REVERT: K 200 LEU cc_start: 0.9080 (mp) cc_final: 0.8556 (mt) REVERT: L 3 ASP cc_start: 0.7438 (t0) cc_final: 0.6599 (t70) REVERT: L 47 ASP cc_start: 0.8976 (p0) cc_final: 0.8464 (p0) REVERT: L 55 ASN cc_start: 0.8999 (t0) cc_final: 0.8600 (t0) REVERT: L 152 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8775 (mt) REVERT: L 213 MET cc_start: 0.8406 (mmm) cc_final: 0.7387 (mmm) outliers start: 54 outliers final: 31 residues processed: 577 average time/residue: 0.3091 time to fit residues: 273.3791 Evaluate side-chains 557 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 519 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 232 PHE Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 232 PHE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 232 PHE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 232 PHE Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain L residue 232 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 0.8980 chunk 24 optimal weight: 0.0070 chunk 125 optimal weight: 10.0000 chunk 161 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 219 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 133 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN E 81 GLN G 81 GLN I 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21204 Z= 0.170 Angle : 0.538 9.480 28056 Z= 0.269 Chirality : 0.039 0.182 3024 Planarity : 0.003 0.029 3204 Dihedral : 8.317 59.982 3852 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.71 % Allowed : 24.29 % Favored : 73.00 % 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: 1.45 (0.18), residues: 2304 helix: 1.87 (0.13), residues: 1560 sheet: 1.69 (0.48), residues: 132 loop : -1.69 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 45 HIS 0.002 0.000 HIS J 95 PHE 0.021 0.001 PHE C 30 TYR 0.025 0.001 TYR H 155 ARG 0.002 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 529 time to evaluate : 2.057 Fit side-chains revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7399 (t0) cc_final: 0.6767 (t70) REVERT: A 47 ASP cc_start: 0.8952 (p0) cc_final: 0.8269 (p0) REVERT: A 55 ASN cc_start: 0.9047 (t0) cc_final: 0.8512 (t0) REVERT: A 213 MET cc_start: 0.8499 (mmm) cc_final: 0.7412 (mmm) REVERT: B 3 ASP cc_start: 0.7422 (t0) cc_final: 0.6634 (t70) REVERT: B 47 ASP cc_start: 0.8988 (p0) cc_final: 0.8480 (p0) REVERT: B 55 ASN cc_start: 0.9045 (t0) cc_final: 0.8673 (t0) REVERT: B 103 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8212 (mp0) REVERT: B 152 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8790 (mt) REVERT: B 213 MET cc_start: 0.8401 (mmm) cc_final: 0.7478 (mmm) REVERT: C 3 ASP cc_start: 0.7481 (t0) cc_final: 0.6735 (t70) REVERT: C 42 GLU cc_start: 0.7760 (tp30) cc_final: 0.7544 (tp30) REVERT: C 47 ASP cc_start: 0.8888 (p0) cc_final: 0.8255 (p0) REVERT: C 55 ASN cc_start: 0.9014 (t0) cc_final: 0.8748 (t0) REVERT: C 76 ARG cc_start: 0.8918 (mtt90) cc_final: 0.8587 (mtt90) REVERT: C 103 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8707 (mm-30) REVERT: C 152 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8746 (mt) REVERT: C 162 LYS cc_start: 0.7489 (mtpt) cc_final: 0.7251 (mtpp) REVERT: D 3 ASP cc_start: 0.7545 (t0) cc_final: 0.6920 (t70) REVERT: D 47 ASP cc_start: 0.8933 (p0) cc_final: 0.8380 (p0) REVERT: D 55 ASN cc_start: 0.9047 (t0) cc_final: 0.8524 (t0) REVERT: E 3 ASP cc_start: 0.7599 (t0) cc_final: 0.7165 (t70) REVERT: E 47 ASP cc_start: 0.9088 (p0) cc_final: 0.8695 (p0) REVERT: E 55 ASN cc_start: 0.9037 (t0) cc_final: 0.8705 (t0) REVERT: E 152 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8755 (mt) REVERT: F 3 ASP cc_start: 0.7495 (t0) cc_final: 0.6755 (t70) REVERT: F 47 ASP cc_start: 0.8916 (p0) cc_final: 0.8264 (p0) REVERT: F 55 ASN cc_start: 0.9025 (t0) cc_final: 0.8804 (t0) REVERT: F 76 ARG cc_start: 0.8931 (mtt90) cc_final: 0.8589 (mtt90) REVERT: F 152 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8649 (mt) REVERT: F 166 GLU cc_start: 0.8582 (tp30) cc_final: 0.8331 (tp30) REVERT: F 213 MET cc_start: 0.8328 (mmm) cc_final: 0.7501 (mmm) REVERT: G 3 ASP cc_start: 0.7298 (t0) cc_final: 0.6661 (t70) REVERT: G 47 ASP cc_start: 0.8877 (p0) cc_final: 0.8203 (p0) REVERT: G 55 ASN cc_start: 0.9053 (t0) cc_final: 0.8841 (t0) REVERT: G 103 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8307 (mp0) REVERT: G 213 MET cc_start: 0.8394 (mmm) cc_final: 0.7513 (mmm) REVERT: H 3 ASP cc_start: 0.7369 (t0) cc_final: 0.6785 (t70) REVERT: H 47 ASP cc_start: 0.8948 (p0) cc_final: 0.8429 (p0) REVERT: H 55 ASN cc_start: 0.9057 (t0) cc_final: 0.8602 (t0) REVERT: H 103 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8224 (mp0) REVERT: I 3 ASP cc_start: 0.7539 (t0) cc_final: 0.6759 (t70) REVERT: I 55 ASN cc_start: 0.9054 (t0) cc_final: 0.8724 (t0) REVERT: I 103 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8179 (mp0) REVERT: I 152 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8736 (mt) REVERT: I 162 LYS cc_start: 0.7466 (mtpt) cc_final: 0.7191 (mtpp) REVERT: J 3 ASP cc_start: 0.7529 (t0) cc_final: 0.6816 (t70) REVERT: J 47 ASP cc_start: 0.8926 (p0) cc_final: 0.8277 (p0) REVERT: J 55 ASN cc_start: 0.9076 (t0) cc_final: 0.8854 (t0) REVERT: J 76 ARG cc_start: 0.8915 (mtt90) cc_final: 0.8568 (mtt90) REVERT: J 152 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8640 (mt) REVERT: J 166 GLU cc_start: 0.8616 (tp30) cc_final: 0.8365 (tp30) REVERT: J 213 MET cc_start: 0.8325 (mmm) cc_final: 0.7497 (mmm) REVERT: K 3 ASP cc_start: 0.7520 (t0) cc_final: 0.6897 (t70) REVERT: K 47 ASP cc_start: 0.8868 (p0) cc_final: 0.8289 (p0) REVERT: K 55 ASN cc_start: 0.9069 (t0) cc_final: 0.8621 (t0) REVERT: K 213 MET cc_start: 0.8423 (mmm) cc_final: 0.7344 (mmm) REVERT: L 3 ASP cc_start: 0.7483 (t0) cc_final: 0.6662 (t70) REVERT: L 47 ASP cc_start: 0.8976 (p0) cc_final: 0.8242 (p0) REVERT: L 55 ASN cc_start: 0.9034 (t0) cc_final: 0.8649 (t0) REVERT: L 100 MET cc_start: 0.9624 (ttp) cc_final: 0.9380 (ttp) REVERT: L 103 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8283 (mp0) REVERT: L 152 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8787 (mt) REVERT: L 161 PHE cc_start: 0.8617 (m-80) cc_final: 0.8410 (m-80) REVERT: L 213 MET cc_start: 0.8397 (mmm) cc_final: 0.7300 (mmm) outliers start: 57 outliers final: 38 residues processed: 546 average time/residue: 0.3116 time to fit residues: 258.7309 Evaluate side-chains 562 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 517 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 232 PHE Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 232 PHE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 232 PHE Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 232 PHE Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain L residue 232 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 131 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 0.0270 chunk 42 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 overall best weight: 1.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN E 81 GLN G 81 GLN G 224 ASN I 81 GLN K 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21204 Z= 0.194 Angle : 0.554 10.102 28056 Z= 0.276 Chirality : 0.039 0.174 3024 Planarity : 0.003 0.029 3204 Dihedral : 8.478 59.212 3852 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.76 % Allowed : 24.38 % Favored : 72.86 % 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: 1.30 (0.17), residues: 2304 helix: 1.78 (0.13), residues: 1584 sheet: 1.67 (0.47), residues: 132 loop : -2.00 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 45 HIS 0.002 0.001 HIS J 95 PHE 0.014 0.001 PHE C 30 TYR 0.020 0.001 TYR H 155 ARG 0.002 0.000 ARG I 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 537 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7426 (t0) cc_final: 0.6781 (t70) REVERT: A 47 ASP cc_start: 0.8953 (p0) cc_final: 0.8278 (p0) REVERT: A 55 ASN cc_start: 0.9070 (t0) cc_final: 0.8625 (t0) REVERT: A 161 PHE cc_start: 0.8636 (m-80) cc_final: 0.8367 (m-80) REVERT: A 213 MET cc_start: 0.8459 (mmm) cc_final: 0.7342 (mmm) REVERT: B 3 ASP cc_start: 0.7459 (t0) cc_final: 0.6679 (t70) REVERT: B 47 ASP cc_start: 0.9013 (p0) cc_final: 0.8504 (p0) REVERT: B 55 ASN cc_start: 0.9069 (t0) cc_final: 0.8726 (t0) REVERT: B 103 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8198 (mp0) REVERT: B 152 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8766 (mt) REVERT: B 162 LYS cc_start: 0.7436 (mtpt) cc_final: 0.7160 (mtpp) REVERT: B 213 MET cc_start: 0.8378 (mmm) cc_final: 0.7281 (mmm) REVERT: C 3 ASP cc_start: 0.7501 (t0) cc_final: 0.6755 (t70) REVERT: C 42 GLU cc_start: 0.7779 (tp30) cc_final: 0.7563 (tp30) REVERT: C 47 ASP cc_start: 0.8900 (p0) cc_final: 0.8264 (p0) REVERT: C 55 ASN cc_start: 0.9036 (t0) cc_final: 0.8780 (t0) REVERT: C 103 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8711 (mm-30) REVERT: C 152 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8761 (mt) REVERT: C 162 LYS cc_start: 0.7490 (mtpt) cc_final: 0.7266 (mtpp) REVERT: D 3 ASP cc_start: 0.7527 (t0) cc_final: 0.6901 (t70) REVERT: D 47 ASP cc_start: 0.8935 (p0) cc_final: 0.8367 (p0) REVERT: D 55 ASN cc_start: 0.9067 (t0) cc_final: 0.8546 (t0) REVERT: D 213 MET cc_start: 0.8461 (mmm) cc_final: 0.7386 (mmm) REVERT: E 3 ASP cc_start: 0.7596 (t0) cc_final: 0.7149 (t70) REVERT: E 47 ASP cc_start: 0.9094 (p0) cc_final: 0.8682 (p0) REVERT: E 55 ASN cc_start: 0.9050 (t0) cc_final: 0.8723 (t0) REVERT: E 152 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8756 (mt) REVERT: E 161 PHE cc_start: 0.8703 (m-80) cc_final: 0.8428 (m-80) REVERT: F 3 ASP cc_start: 0.7513 (t0) cc_final: 0.6769 (t70) REVERT: F 47 ASP cc_start: 0.8925 (p0) cc_final: 0.8277 (p0) REVERT: F 55 ASN cc_start: 0.9046 (t0) cc_final: 0.8827 (t0) REVERT: F 152 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8667 (mt) REVERT: G 3 ASP cc_start: 0.7377 (t0) cc_final: 0.6736 (t70) REVERT: G 47 ASP cc_start: 0.8880 (p0) cc_final: 0.8207 (p0) REVERT: G 55 ASN cc_start: 0.9054 (t0) cc_final: 0.8836 (t0) REVERT: G 213 MET cc_start: 0.8409 (mmm) cc_final: 0.7512 (mmm) REVERT: H 3 ASP cc_start: 0.7422 (t0) cc_final: 0.6819 (t70) REVERT: H 47 ASP cc_start: 0.8948 (p0) cc_final: 0.8448 (p0) REVERT: H 55 ASN cc_start: 0.9088 (t0) cc_final: 0.8638 (t0) REVERT: H 103 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8222 (mp0) REVERT: H 161 PHE cc_start: 0.8608 (m-80) cc_final: 0.8391 (m-80) REVERT: H 162 LYS cc_start: 0.7436 (mtpt) cc_final: 0.7124 (mtpp) REVERT: I 3 ASP cc_start: 0.7559 (t0) cc_final: 0.6764 (t70) REVERT: I 47 ASP cc_start: 0.8844 (p0) cc_final: 0.8079 (p0) REVERT: I 55 ASN cc_start: 0.9071 (t0) cc_final: 0.8748 (t0) REVERT: I 152 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8739 (mt) REVERT: I 161 PHE cc_start: 0.8622 (m-80) cc_final: 0.8384 (m-80) REVERT: I 162 LYS cc_start: 0.7490 (mtpt) cc_final: 0.7222 (mtpp) REVERT: J 3 ASP cc_start: 0.7538 (t0) cc_final: 0.6803 (t70) REVERT: J 47 ASP cc_start: 0.8942 (p0) cc_final: 0.8298 (p0) REVERT: J 55 ASN cc_start: 0.9094 (t0) cc_final: 0.8876 (t0) REVERT: J 152 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8655 (mt) REVERT: J 166 GLU cc_start: 0.8612 (tp30) cc_final: 0.8353 (tp30) REVERT: K 3 ASP cc_start: 0.7532 (t0) cc_final: 0.6902 (t70) REVERT: K 47 ASP cc_start: 0.8884 (p0) cc_final: 0.8281 (p0) REVERT: K 55 ASN cc_start: 0.9086 (t0) cc_final: 0.8625 (t0) REVERT: K 213 MET cc_start: 0.8445 (mmm) cc_final: 0.7345 (mmm) REVERT: L 3 ASP cc_start: 0.7523 (t0) cc_final: 0.6702 (t70) REVERT: L 47 ASP cc_start: 0.8979 (p0) cc_final: 0.8462 (p0) REVERT: L 55 ASN cc_start: 0.9058 (t0) cc_final: 0.8704 (t0) REVERT: L 152 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8771 (mt) REVERT: L 162 LYS cc_start: 0.7399 (mtpt) cc_final: 0.7119 (mtpp) REVERT: L 213 MET cc_start: 0.8354 (mmm) cc_final: 0.7214 (mmm) outliers start: 58 outliers final: 39 residues processed: 554 average time/residue: 0.3351 time to fit residues: 282.0772 Evaluate side-chains 567 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 521 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 232 PHE Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 232 PHE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 232 PHE Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 152 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 2.9990 chunk 210 optimal weight: 8.9990 chunk 192 optimal weight: 0.7980 chunk 204 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN E 81 GLN G 81 GLN I 81 GLN K 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21204 Z= 0.195 Angle : 0.565 10.745 28056 Z= 0.280 Chirality : 0.039 0.185 3024 Planarity : 0.003 0.029 3204 Dihedral : 8.513 59.530 3852 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.52 % Allowed : 24.76 % Favored : 72.71 % 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: 1.29 (0.17), residues: 2304 helix: 1.82 (0.13), residues: 1572 sheet: 1.62 (0.48), residues: 132 loop : -2.04 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 45 HIS 0.002 0.001 HIS J 95 PHE 0.014 0.001 PHE C 30 TYR 0.021 0.001 TYR G 230 ARG 0.002 0.000 ARG E 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 524 time to evaluate : 2.227 Fit side-chains revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7433 (t0) cc_final: 0.6778 (t70) REVERT: A 47 ASP cc_start: 0.8948 (p0) cc_final: 0.8282 (p0) REVERT: A 55 ASN cc_start: 0.9062 (t0) cc_final: 0.8617 (t0) REVERT: A 213 MET cc_start: 0.8444 (mmm) cc_final: 0.7318 (mmm) REVERT: B 3 ASP cc_start: 0.7451 (t0) cc_final: 0.6660 (t70) REVERT: B 47 ASP cc_start: 0.9004 (p0) cc_final: 0.8478 (p0) REVERT: B 55 ASN cc_start: 0.9068 (t0) cc_final: 0.8725 (t0) REVERT: B 103 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8189 (mp0) REVERT: B 152 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8762 (mt) REVERT: B 162 LYS cc_start: 0.7433 (mtpt) cc_final: 0.7138 (mtpp) REVERT: B 213 MET cc_start: 0.8373 (mmm) cc_final: 0.7264 (mmm) REVERT: C 3 ASP cc_start: 0.7503 (t0) cc_final: 0.6749 (t70) REVERT: C 42 GLU cc_start: 0.7805 (tp30) cc_final: 0.7582 (tp30) REVERT: C 47 ASP cc_start: 0.8890 (p0) cc_final: 0.8268 (p0) REVERT: C 55 ASN cc_start: 0.9046 (t0) cc_final: 0.8794 (t0) REVERT: C 76 ARG cc_start: 0.8936 (mtt90) cc_final: 0.8662 (mtt90) REVERT: C 103 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8717 (mm-30) REVERT: C 152 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8755 (mt) REVERT: C 162 LYS cc_start: 0.7501 (mtpt) cc_final: 0.7277 (mtpp) REVERT: C 213 MET cc_start: 0.8358 (mmm) cc_final: 0.7271 (mmm) REVERT: D 3 ASP cc_start: 0.7509 (t0) cc_final: 0.6866 (t70) REVERT: D 47 ASP cc_start: 0.8940 (p0) cc_final: 0.8376 (p0) REVERT: D 55 ASN cc_start: 0.9069 (t0) cc_final: 0.8544 (t0) REVERT: D 161 PHE cc_start: 0.8644 (m-80) cc_final: 0.8383 (m-80) REVERT: D 213 MET cc_start: 0.8449 (mmm) cc_final: 0.7369 (mmm) REVERT: E 3 ASP cc_start: 0.7587 (t0) cc_final: 0.7122 (t70) REVERT: E 47 ASP cc_start: 0.9052 (p0) cc_final: 0.8632 (p0) REVERT: E 55 ASN cc_start: 0.9047 (t0) cc_final: 0.8723 (t0) REVERT: E 152 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8754 (mt) REVERT: F 3 ASP cc_start: 0.7509 (t0) cc_final: 0.6760 (t70) REVERT: F 47 ASP cc_start: 0.8930 (p0) cc_final: 0.8282 (p0) REVERT: F 55 ASN cc_start: 0.9042 (t0) cc_final: 0.8821 (t0) REVERT: F 152 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8669 (mt) REVERT: F 213 MET cc_start: 0.8374 (mmm) cc_final: 0.7624 (mmm) REVERT: G 3 ASP cc_start: 0.7419 (t0) cc_final: 0.6749 (t70) REVERT: G 47 ASP cc_start: 0.8875 (p0) cc_final: 0.8214 (p0) REVERT: G 55 ASN cc_start: 0.9043 (t0) cc_final: 0.8825 (t0) REVERT: H 3 ASP cc_start: 0.7456 (t0) cc_final: 0.6833 (t70) REVERT: H 47 ASP cc_start: 0.8948 (p0) cc_final: 0.8447 (p0) REVERT: H 55 ASN cc_start: 0.9085 (t0) cc_final: 0.8640 (t0) REVERT: H 161 PHE cc_start: 0.8617 (m-80) cc_final: 0.8381 (m-80) REVERT: H 162 LYS cc_start: 0.7452 (mtpt) cc_final: 0.7183 (mtpp) REVERT: H 213 MET cc_start: 0.8485 (mmm) cc_final: 0.7703 (mmm) REVERT: I 3 ASP cc_start: 0.7551 (t0) cc_final: 0.6749 (t70) REVERT: I 47 ASP cc_start: 0.8848 (p0) cc_final: 0.8099 (p0) REVERT: I 55 ASN cc_start: 0.9070 (t0) cc_final: 0.8768 (t0) REVERT: I 103 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8156 (mp0) REVERT: I 152 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8732 (mt) REVERT: I 213 MET cc_start: 0.8419 (mmm) cc_final: 0.7264 (mmm) REVERT: J 3 ASP cc_start: 0.7527 (t0) cc_final: 0.6766 (t70) REVERT: J 47 ASP cc_start: 0.8938 (p0) cc_final: 0.8302 (p0) REVERT: J 55 ASN cc_start: 0.9091 (t0) cc_final: 0.8876 (t0) REVERT: J 152 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8661 (mt) REVERT: J 166 GLU cc_start: 0.8611 (tp30) cc_final: 0.8366 (tp30) REVERT: J 213 MET cc_start: 0.8383 (mmm) cc_final: 0.7632 (mmm) REVERT: K 3 ASP cc_start: 0.7516 (t0) cc_final: 0.6890 (t70) REVERT: K 47 ASP cc_start: 0.8880 (p0) cc_final: 0.8424 (p0) REVERT: K 55 ASN cc_start: 0.9088 (t0) cc_final: 0.8620 (t0) REVERT: K 161 PHE cc_start: 0.8651 (m-80) cc_final: 0.8397 (m-80) REVERT: L 3 ASP cc_start: 0.7504 (t0) cc_final: 0.6690 (t70) REVERT: L 47 ASP cc_start: 0.8984 (p0) cc_final: 0.8453 (p0) REVERT: L 55 ASN cc_start: 0.9061 (t0) cc_final: 0.8699 (t0) REVERT: L 103 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8240 (mp0) REVERT: L 152 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8771 (mt) REVERT: L 162 LYS cc_start: 0.7402 (mtpt) cc_final: 0.7127 (mtpp) REVERT: L 213 MET cc_start: 0.8412 (mmm) cc_final: 0.7341 (mmm) outliers start: 53 outliers final: 38 residues processed: 538 average time/residue: 0.3134 time to fit residues: 256.9114 Evaluate side-chains 559 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 514 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 232 PHE Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 232 PHE Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 232 PHE Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 227 optimal weight: 1.9990 chunk 209 optimal weight: 7.9990 chunk 180 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 110 optimal weight: 20.0000 chunk 143 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN C 81 GLN E 81 GLN G 81 GLN I 81 GLN K 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21204 Z= 0.149 Angle : 0.556 11.231 28056 Z= 0.274 Chirality : 0.039 0.181 3024 Planarity : 0.003 0.030 3204 Dihedral : 8.147 57.604 3852 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.10 % Allowed : 25.48 % Favored : 72.43 % 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: 1.33 (0.17), residues: 2304 helix: 1.85 (0.13), residues: 1572 sheet: 1.68 (0.48), residues: 132 loop : -2.03 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP G 45 HIS 0.002 0.000 HIS J 95 PHE 0.015 0.001 PHE C 30 TYR 0.022 0.001 TYR B 230 ARG 0.002 0.000 ARG B 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 542 time to evaluate : 2.221 Fit side-chains revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7420 (t0) cc_final: 0.6836 (t70) REVERT: A 47 ASP cc_start: 0.8895 (p0) cc_final: 0.8273 (p0) REVERT: A 55 ASN cc_start: 0.8995 (t0) cc_final: 0.8474 (t0) REVERT: A 161 PHE cc_start: 0.8576 (m-80) cc_final: 0.8351 (m-80) REVERT: A 213 MET cc_start: 0.8399 (mmm) cc_final: 0.7230 (mmm) REVERT: B 3 ASP cc_start: 0.7410 (t0) cc_final: 0.6587 (t70) REVERT: B 47 ASP cc_start: 0.8980 (p0) cc_final: 0.8455 (p0) REVERT: B 55 ASN cc_start: 0.9012 (t0) cc_final: 0.8670 (t0) REVERT: B 103 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8151 (mp0) REVERT: B 152 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8780 (mt) REVERT: B 213 MET cc_start: 0.8361 (mmm) cc_final: 0.7207 (mmm) REVERT: C 3 ASP cc_start: 0.7472 (t0) cc_final: 0.6792 (t70) REVERT: C 42 GLU cc_start: 0.7792 (tp30) cc_final: 0.7589 (tp30) REVERT: C 47 ASP cc_start: 0.8849 (p0) cc_final: 0.8272 (p0) REVERT: C 55 ASN cc_start: 0.8988 (t0) cc_final: 0.8731 (t0) REVERT: C 76 ARG cc_start: 0.8871 (mtt90) cc_final: 0.8616 (mtt90) REVERT: C 152 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8756 (mt) REVERT: C 162 LYS cc_start: 0.7464 (mtpt) cc_final: 0.7194 (mtpp) REVERT: C 213 MET cc_start: 0.8357 (mmm) cc_final: 0.7293 (mmm) REVERT: D 3 ASP cc_start: 0.7457 (t0) cc_final: 0.6810 (t70) REVERT: D 47 ASP cc_start: 0.8885 (p0) cc_final: 0.8368 (p0) REVERT: D 55 ASN cc_start: 0.9006 (t0) cc_final: 0.8486 (t0) REVERT: D 161 PHE cc_start: 0.8592 (m-80) cc_final: 0.8331 (m-80) REVERT: D 213 MET cc_start: 0.8421 (mmm) cc_final: 0.7320 (mmm) REVERT: E 3 ASP cc_start: 0.7525 (t0) cc_final: 0.6774 (t70) REVERT: E 47 ASP cc_start: 0.9056 (p0) cc_final: 0.8601 (p0) REVERT: E 55 ASN cc_start: 0.8987 (t0) cc_final: 0.8663 (t0) REVERT: E 152 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8734 (mt) REVERT: E 161 PHE cc_start: 0.8665 (m-80) cc_final: 0.8445 (m-80) REVERT: F 3 ASP cc_start: 0.7489 (t0) cc_final: 0.6741 (t70) REVERT: F 47 ASP cc_start: 0.8887 (p0) cc_final: 0.8270 (p0) REVERT: F 55 ASN cc_start: 0.8987 (t0) cc_final: 0.8762 (t0) REVERT: F 76 ARG cc_start: 0.8853 (mtt90) cc_final: 0.8610 (mtt90) REVERT: F 152 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8660 (mt) REVERT: F 162 LYS cc_start: 0.7401 (mtpt) cc_final: 0.7127 (mtpp) REVERT: F 213 MET cc_start: 0.8402 (mmm) cc_final: 0.7657 (mmm) REVERT: G 3 ASP cc_start: 0.7404 (t0) cc_final: 0.6700 (t70) REVERT: G 47 ASP cc_start: 0.8812 (p0) cc_final: 0.8193 (p0) REVERT: G 55 ASN cc_start: 0.8988 (t0) cc_final: 0.8768 (t0) REVERT: H 3 ASP cc_start: 0.7425 (t0) cc_final: 0.6785 (t70) REVERT: H 47 ASP cc_start: 0.8898 (p0) cc_final: 0.8381 (p0) REVERT: H 55 ASN cc_start: 0.9026 (t0) cc_final: 0.8578 (t0) REVERT: H 161 PHE cc_start: 0.8574 (m-80) cc_final: 0.8346 (m-80) REVERT: I 3 ASP cc_start: 0.7520 (t0) cc_final: 0.6708 (t70) REVERT: I 47 ASP cc_start: 0.8825 (p0) cc_final: 0.8116 (p0) REVERT: I 55 ASN cc_start: 0.9018 (t0) cc_final: 0.8690 (t0) REVERT: I 152 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8723 (mt) REVERT: I 162 LYS cc_start: 0.7432 (mtpt) cc_final: 0.7156 (mtpp) REVERT: I 213 MET cc_start: 0.8417 (mmm) cc_final: 0.7271 (mmm) REVERT: J 3 ASP cc_start: 0.7502 (t0) cc_final: 0.6710 (t70) REVERT: J 47 ASP cc_start: 0.8895 (p0) cc_final: 0.8292 (p0) REVERT: J 55 ASN cc_start: 0.9046 (t0) cc_final: 0.8827 (t0) REVERT: J 76 ARG cc_start: 0.8858 (mtt90) cc_final: 0.8585 (mtt90) REVERT: J 152 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8657 (mt) REVERT: J 166 GLU cc_start: 0.8596 (tp30) cc_final: 0.8361 (tp30) REVERT: J 213 MET cc_start: 0.8399 (mmm) cc_final: 0.7648 (mmm) REVERT: K 3 ASP cc_start: 0.7471 (t0) cc_final: 0.6822 (t70) REVERT: K 47 ASP cc_start: 0.8818 (p0) cc_final: 0.8358 (p0) REVERT: K 55 ASN cc_start: 0.9030 (t0) cc_final: 0.8488 (t0) REVERT: K 161 PHE cc_start: 0.8612 (m-80) cc_final: 0.8361 (m-80) REVERT: K 213 MET cc_start: 0.8439 (mmm) cc_final: 0.7371 (mmm) REVERT: L 3 ASP cc_start: 0.7482 (t0) cc_final: 0.6648 (t70) REVERT: L 47 ASP cc_start: 0.8969 (p0) cc_final: 0.8439 (p0) REVERT: L 55 ASN cc_start: 0.9001 (t0) cc_final: 0.8637 (t0) REVERT: L 103 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8203 (mp0) REVERT: L 152 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8786 (mt) REVERT: L 213 MET cc_start: 0.8341 (mmm) cc_final: 0.7169 (mmm) outliers start: 44 outliers final: 35 residues processed: 554 average time/residue: 0.3174 time to fit residues: 266.5170 Evaluate side-chains 562 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 520 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 232 PHE Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 232 PHE Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 232 PHE Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.0570 chunk 55 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 181 optimal weight: 0.0670 chunk 75 optimal weight: 0.8980 chunk 186 optimal weight: 0.0870 chunk 22 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 overall best weight: 0.4014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN E 81 GLN H 224 ASN K 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.139100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.119397 restraints weight = 34346.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.123114 restraints weight = 13913.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.125517 restraints weight = 7433.751| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21204 Z= 0.134 Angle : 0.562 11.130 28056 Z= 0.274 Chirality : 0.039 0.174 3024 Planarity : 0.003 0.030 3204 Dihedral : 7.693 56.930 3852 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.10 % Allowed : 25.81 % Favored : 72.10 % 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: 1.36 (0.17), residues: 2304 helix: 1.86 (0.13), residues: 1572 sheet: 1.74 (0.48), residues: 132 loop : -2.01 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP K 25 HIS 0.005 0.000 HIS J 95 PHE 0.015 0.001 PHE C 30 TYR 0.033 0.001 TYR I 155 ARG 0.002 0.000 ARG B 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5713.43 seconds wall clock time: 104 minutes 1.39 seconds (6241.39 seconds total)