Starting phenix.real_space_refine on Mon Dec 30 23:00:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tu7_41618/12_2024/8tu7_41618.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tu7_41618/12_2024/8tu7_41618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tu7_41618/12_2024/8tu7_41618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tu7_41618/12_2024/8tu7_41618.map" model { file = "/net/cci-nas-00/data/ceres_data/8tu7_41618/12_2024/8tu7_41618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tu7_41618/12_2024/8tu7_41618.cif" } resolution = 2.5 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= 0.101 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 6 7.16 5 Zn 24 6.06 5 S 192 5.16 5 C 21216 2.51 5 N 5928 2.21 5 O 6480 1.98 5 H 32400 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 322 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 66246 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "B" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "C" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "D" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "E" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "F" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "G" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "H" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "I" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "J" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "K" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "L" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "M" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "N" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "O" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "P" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Q" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "R" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "S" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "T" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "U" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "V" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "W" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "X" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 26.21, per 1000 atoms: 0.40 Number of scatterers: 66246 At special positions: 0 Unit cell: (131.37, 131.37, 132.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 24 29.99 Fe 6 26.01 S 192 16.00 O 6480 8.00 N 5928 7.00 C 21216 6.00 H 32400 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.68 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 202 " pdb="ZN ZN A 202 " - pdb=" ND1 HIS A 65 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" ND1 HIS B 65 " pdb=" ZN C 202 " pdb="ZN ZN C 202 " - pdb=" ND1 HIS C 65 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" ND1 HIS D 65 " pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" ND1 HIS E 65 " pdb=" ZN F 201 " pdb="ZN ZN F 201 " - pdb=" ND1 HIS F 65 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" ND1 HIS G 65 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" ND1 HIS H 65 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" ND1 HIS I 65 " pdb=" ZN J 201 " pdb="ZN ZN J 201 " - pdb=" ND1 HIS J 65 " pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" ND1 HIS K 65 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" ND1 HIS L 65 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" ND1 HIS M 65 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" ND1 HIS N 65 " pdb=" ZN O 201 " pdb="ZN ZN O 201 " - pdb=" ND1 HIS O 65 " pdb=" ZN P 201 " pdb="ZN ZN P 201 " - pdb=" ND1 HIS P 65 " pdb=" ZN Q 202 " pdb="ZN ZN Q 202 " - pdb=" ND1 HIS Q 65 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 65 " pdb=" ZN S 201 " pdb="ZN ZN S 201 " - pdb=" ND1 HIS S 65 " pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" ND1 HIS T 65 " pdb=" ZN U 201 " pdb="ZN ZN U 201 " - pdb=" ND1 HIS U 65 " pdb=" ZN V 201 " pdb="ZN ZN V 201 " - pdb=" ND1 HIS V 65 " pdb=" ZN W 201 " pdb="ZN ZN W 201 " - pdb=" ND1 HIS W 65 " pdb=" ZN X 201 " pdb="ZN ZN X 201 " - pdb=" ND1 HIS X 65 " 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 76 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 163 through 174 removed outlier: 3.932A pdb=" N GLU A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 163 through 174 removed outlier: 3.929A pdb=" N GLU B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 42 Processing helix chain 'C' and resid 48 through 76 Processing helix chain 'C' and resid 95 through 124 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 137 through 159 Processing helix chain 'C' and resid 163 through 174 removed outlier: 3.946A pdb=" N GLU C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 42 Processing helix chain 'D' and resid 48 through 76 Processing helix chain 'D' and resid 95 through 124 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 137 through 159 Processing helix chain 'D' and resid 163 through 174 removed outlier: 3.961A pdb=" N GLU D 167 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 76 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 163 through 174 removed outlier: 4.008A pdb=" N GLU E 167 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR E 168 " --> pdb=" O GLY E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 163 through 174 removed outlier: 3.942A pdb=" N GLU F 167 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 163 through 174 removed outlier: 3.967A pdb=" N GLU G 167 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR G 168 " --> pdb=" O GLY G 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 76 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 163 through 174 removed outlier: 3.959A pdb=" N GLU H 167 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR H 168 " --> pdb=" O GLY H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 76 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 163 through 174 removed outlier: 3.943A pdb=" N GLU I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR I 168 " --> pdb=" O GLY I 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 42 Processing helix chain 'J' and resid 48 through 76 Processing helix chain 'J' and resid 95 through 124 Processing helix chain 'J' and resid 126 through 137 Processing helix chain 'J' and resid 137 through 159 Processing helix chain 'J' and resid 163 through 174 removed outlier: 3.945A pdb=" N GLU J 167 " --> pdb=" O ALA J 163 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 76 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 163 through 174 removed outlier: 3.960A pdb=" N GLU K 167 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR K 168 " --> pdb=" O GLY K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 42 Processing helix chain 'L' and resid 48 through 76 Processing helix chain 'L' and resid 95 through 124 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 137 through 159 Processing helix chain 'L' and resid 163 through 174 removed outlier: 3.976A pdb=" N GLU L 167 " --> pdb=" O ALA L 163 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR L 168 " --> pdb=" O GLY L 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 163 through 174 removed outlier: 3.944A pdb=" N GLU M 167 " --> pdb=" O ALA M 163 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR M 168 " --> pdb=" O GLY M 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 42 Processing helix chain 'N' and resid 48 through 76 Processing helix chain 'N' and resid 95 through 124 Processing helix chain 'N' and resid 126 through 137 Processing helix chain 'N' and resid 137 through 159 Processing helix chain 'N' and resid 163 through 174 removed outlier: 3.943A pdb=" N GLU N 167 " --> pdb=" O ALA N 163 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR N 168 " --> pdb=" O GLY N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 76 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 163 through 174 removed outlier: 3.978A pdb=" N GLU O 167 " --> pdb=" O ALA O 163 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR O 168 " --> pdb=" O GLY O 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 76 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 163 through 174 removed outlier: 3.959A pdb=" N GLU P 167 " --> pdb=" O ALA P 163 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR P 168 " --> pdb=" O GLY P 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 163 through 174 removed outlier: 3.907A pdb=" N GLU Q 167 " --> pdb=" O ALA Q 163 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR Q 168 " --> pdb=" O GLY Q 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 42 Processing helix chain 'R' and resid 48 through 76 Processing helix chain 'R' and resid 95 through 124 Processing helix chain 'R' and resid 126 through 137 Processing helix chain 'R' and resid 137 through 159 Processing helix chain 'R' and resid 163 through 174 removed outlier: 3.954A pdb=" N GLU R 167 " --> pdb=" O ALA R 163 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR R 168 " --> pdb=" O GLY R 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 76 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 163 through 174 removed outlier: 3.966A pdb=" N GLU S 167 " --> pdb=" O ALA S 163 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR S 168 " --> pdb=" O GLY S 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 42 Processing helix chain 'T' and resid 48 through 76 Processing helix chain 'T' and resid 95 through 124 Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 137 through 159 Processing helix chain 'T' and resid 163 through 174 removed outlier: 3.968A pdb=" N GLU T 167 " --> pdb=" O ALA T 163 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR T 168 " --> pdb=" O GLY T 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 42 Processing helix chain 'U' and resid 48 through 76 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 163 through 174 removed outlier: 3.942A pdb=" N GLU U 167 " --> pdb=" O ALA U 163 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR U 168 " --> pdb=" O GLY U 164 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 42 Processing helix chain 'V' and resid 48 through 76 Processing helix chain 'V' and resid 95 through 124 Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 137 through 159 Processing helix chain 'V' and resid 163 through 174 removed outlier: 3.948A pdb=" N GLU V 167 " --> pdb=" O ALA V 163 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR V 168 " --> pdb=" O GLY V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 163 through 174 removed outlier: 3.969A pdb=" N GLU W 167 " --> pdb=" O ALA W 163 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR W 168 " --> pdb=" O GLY W 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 76 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 163 through 174 removed outlier: 4.010A pdb=" N GLU X 167 " --> pdb=" O ALA X 163 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR X 168 " --> pdb=" O GLY X 164 " (cutoff:3.500A) 2640 hydrogen bonds defined for protein. 7920 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: 23.41 Time building geometry restraints manager: 16.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 32328 1.03 - 1.23: 124 1.23 - 1.42: 14924 1.42 - 1.62: 19224 1.62 - 1.81: 312 Bond restraints: 66912 Sorted by residual: bond pdb=" CG PRO L 161 " pdb=" CD PRO L 161 " ideal model delta sigma weight residual 1.512 1.482 0.030 2.70e-02 1.37e+03 1.26e+00 bond pdb=" CG PRO Q 161 " pdb=" CD PRO Q 161 " ideal model delta sigma weight residual 1.512 1.482 0.030 2.70e-02 1.37e+03 1.26e+00 bond pdb=" CG PRO U 161 " pdb=" CD PRO U 161 " ideal model delta sigma weight residual 1.512 1.482 0.030 2.70e-02 1.37e+03 1.25e+00 bond pdb=" CG PRO T 161 " pdb=" CD PRO T 161 " ideal model delta sigma weight residual 1.512 1.482 0.030 2.70e-02 1.37e+03 1.24e+00 bond pdb=" CG PRO E 161 " pdb=" CD PRO E 161 " ideal model delta sigma weight residual 1.512 1.482 0.030 2.70e-02 1.37e+03 1.24e+00 ... (remaining 66907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 116223 1.40 - 2.80: 3700 2.80 - 4.20: 337 4.20 - 5.60: 43 5.60 - 7.00: 9 Bond angle restraints: 120312 Sorted by residual: angle pdb=" N VAL S 46 " pdb=" CA VAL S 46 " pdb=" C VAL S 46 " ideal model delta sigma weight residual 111.48 106.80 4.68 9.40e-01 1.13e+00 2.48e+01 angle pdb=" N VAL H 46 " pdb=" CA VAL H 46 " pdb=" C VAL H 46 " ideal model delta sigma weight residual 111.48 106.82 4.66 9.40e-01 1.13e+00 2.45e+01 angle pdb=" N VAL E 46 " pdb=" CA VAL E 46 " pdb=" C VAL E 46 " ideal model delta sigma weight residual 111.48 106.85 4.63 9.40e-01 1.13e+00 2.42e+01 angle pdb=" N VAL O 46 " pdb=" CA VAL O 46 " pdb=" C VAL O 46 " ideal model delta sigma weight residual 111.48 106.85 4.63 9.40e-01 1.13e+00 2.42e+01 angle pdb=" N VAL U 46 " pdb=" CA VAL U 46 " pdb=" C VAL U 46 " ideal model delta sigma weight residual 111.48 106.87 4.61 9.40e-01 1.13e+00 2.41e+01 ... (remaining 120307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 27639 18.07 - 36.14: 2711 36.14 - 54.21: 860 54.21 - 72.27: 287 72.27 - 90.34: 63 Dihedral angle restraints: 31560 sinusoidal: 16920 harmonic: 14640 Sorted by residual: dihedral pdb=" CA TRP A 93 " pdb=" C TRP A 93 " pdb=" N GLU A 94 " pdb=" CA GLU A 94 " ideal model delta harmonic sigma weight residual 180.00 156.04 23.96 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA TRP E 93 " pdb=" C TRP E 93 " pdb=" N GLU E 94 " pdb=" CA GLU E 94 " ideal model delta harmonic sigma weight residual 180.00 156.07 23.93 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA TRP B 93 " pdb=" C TRP B 93 " pdb=" N GLU B 94 " pdb=" CA GLU B 94 " ideal model delta harmonic sigma weight residual 180.00 156.36 23.64 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 31557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 3348 0.032 - 0.064: 1134 0.064 - 0.095: 249 0.095 - 0.127: 115 0.127 - 0.159: 2 Chirality restraints: 4848 Sorted by residual: chirality pdb=" CA GLU U 94 " pdb=" N GLU U 94 " pdb=" C GLU U 94 " pdb=" CB GLU U 94 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA VAL U 46 " pdb=" N VAL U 46 " pdb=" C VAL U 46 " pdb=" CB VAL U 46 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA VAL W 46 " pdb=" N VAL W 46 " pdb=" C VAL W 46 " pdb=" CB VAL W 46 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 4845 not shown) Planarity restraints: 10128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP D 93 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.52e+00 pdb=" C TRP D 93 " 0.021 2.00e-02 2.50e+03 pdb=" O TRP D 93 " -0.008 2.00e-02 2.50e+03 pdb=" N GLU D 94 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 94 " 0.006 2.00e-02 2.50e+03 1.19e-02 1.42e+00 pdb=" C GLU A 94 " -0.021 2.00e-02 2.50e+03 pdb=" O GLU A 94 " 0.008 2.00e-02 2.50e+03 pdb=" N SER A 95 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE I 133 " -0.006 2.00e-02 2.50e+03 1.19e-02 1.41e+00 pdb=" C ILE I 133 " 0.021 2.00e-02 2.50e+03 pdb=" O ILE I 133 " -0.008 2.00e-02 2.50e+03 pdb=" N GLU I 134 " -0.007 2.00e-02 2.50e+03 ... (remaining 10125 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 2477 2.14 - 2.76: 129783 2.76 - 3.37: 220416 3.37 - 3.99: 287342 3.99 - 4.60: 443474 Nonbonded interactions: 1083492 Sorted by model distance: nonbonded pdb=" OE2 GLU K 17 " pdb=" H ARG K 79 " model vdw 1.529 2.450 nonbonded pdb=" OD1 ASP A 84 " pdb=" H LYS L 87 " model vdw 1.538 2.450 nonbonded pdb=" H LYS K 87 " pdb=" OD1 ASP R 84 " model vdw 1.546 2.450 nonbonded pdb=" H LYS F 87 " pdb=" OD1 ASP Q 84 " model vdw 1.547 2.450 nonbonded pdb=" OE2 GLU P 17 " pdb=" H ARG P 79 " model vdw 1.547 2.450 ... (remaining 1083487 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 5 through 176) selection = (chain 'B' and resid 5 through 176) selection = (chain 'C' and resid 5 through 176) selection = (chain 'D' and resid 5 through 176) selection = (chain 'E' and resid 5 through 176) selection = (chain 'F' and resid 5 through 176) selection = (chain 'G' and resid 5 through 176) selection = (chain 'H' and resid 5 through 176) selection = (chain 'I' and resid 5 through 176) selection = (chain 'J' and resid 5 through 176) selection = (chain 'K' and resid 5 through 176) selection = (chain 'L' and resid 5 through 176) selection = (chain 'M' and resid 5 through 176) selection = (chain 'N' and resid 5 through 176) selection = (chain 'O' and resid 5 through 176) selection = (chain 'P' and resid 5 through 176) selection = (chain 'Q' and resid 5 through 176) selection = (chain 'R' and resid 5 through 176) selection = (chain 'S' and resid 5 through 176) selection = (chain 'T' and resid 5 through 176) selection = (chain 'U' and resid 5 through 176) selection = (chain 'V' and resid 5 through 176) selection = (chain 'W' and resid 5 through 176) selection = (chain 'X' and resid 5 through 176) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 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: 0.840 Extract box with map and model: 2.380 Check model and map are aligned: 0.460 Set scattering table: 0.590 Process input model: 129.720 Find NCS groups from input model: 2.580 Set up NCS constraints: 0.440 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: 0.020 Load rotamer database and sin/cos tables:13.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 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 : 0.004 0.042 34512 Z= 0.277 Angle : 0.608 6.998 46416 Z= 0.350 Chirality : 0.036 0.159 4848 Planarity : 0.004 0.037 6096 Dihedral : 18.568 90.342 13080 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.00 % Allowed : 20.15 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.13), residues: 4080 helix: 2.64 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : 0.11 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP I 93 HIS 0.004 0.001 HIS E 173 PHE 0.019 0.002 PHE J 41 TYR 0.016 0.002 TYR T 137 ARG 0.006 0.001 ARG Q 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 674 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 601 time to evaluate : 4.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.6258 (mm-40) cc_final: 0.5368 (pt0) REVERT: A 27 GLU cc_start: 0.5906 (mm-30) cc_final: 0.5230 (mm-30) REVERT: A 53 LYS cc_start: 0.6688 (ttmt) cc_final: 0.5692 (ttpp) REVERT: A 135 THR cc_start: 0.7378 (t) cc_final: 0.7166 (p) REVERT: A 136 TYR cc_start: 0.7791 (m-80) cc_final: 0.7561 (m-80) REVERT: A 140 GLU cc_start: 0.6316 (mm-30) cc_final: 0.5145 (mp0) REVERT: B 53 LYS cc_start: 0.6675 (ttmt) cc_final: 0.5633 (ttpp) REVERT: C 53 LYS cc_start: 0.6716 (ttmt) cc_final: 0.5742 (ttpp) REVERT: C 63 ARG cc_start: 0.6471 (tmm160) cc_final: 0.5638 (tmm160) REVERT: D 53 LYS cc_start: 0.6748 (ttmt) cc_final: 0.5745 (ttpp) REVERT: E 14 GLN cc_start: 0.6174 (mm-40) cc_final: 0.5161 (pt0) REVERT: E 53 LYS cc_start: 0.6697 (ttmt) cc_final: 0.5664 (ttpp) REVERT: E 135 THR cc_start: 0.7539 (t) cc_final: 0.7259 (p) REVERT: F 53 LYS cc_start: 0.6740 (ttmt) cc_final: 0.5744 (ttpp) REVERT: G 140 GLU cc_start: 0.6251 (mm-30) cc_final: 0.5026 (mp0) REVERT: I 14 GLN cc_start: 0.6301 (mm-40) cc_final: 0.5316 (pt0) REVERT: I 53 LYS cc_start: 0.6731 (ttmt) cc_final: 0.5670 (ttpp) REVERT: J 53 LYS cc_start: 0.6715 (ttmt) cc_final: 0.5744 (ttpp) REVERT: K 27 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6592 (mm-30) REVERT: K 53 LYS cc_start: 0.6746 (ttmt) cc_final: 0.5751 (ttpp) REVERT: L 53 LYS cc_start: 0.6751 (ttmt) cc_final: 0.5767 (ttpp) REVERT: M 53 LYS cc_start: 0.6738 (ttmt) cc_final: 0.5713 (ttpp) REVERT: N 53 LYS cc_start: 0.6710 (ttmt) cc_final: 0.5661 (ttpp) REVERT: N 68 LYS cc_start: 0.6949 (OUTLIER) cc_final: 0.6489 (tttt) REVERT: N 135 THR cc_start: 0.7510 (t) cc_final: 0.7266 (p) REVERT: O 53 LYS cc_start: 0.6651 (ttmt) cc_final: 0.5621 (ttpp) REVERT: O 119 LYS cc_start: 0.6498 (tttt) cc_final: 0.6283 (ttmt) REVERT: O 135 THR cc_start: 0.7515 (t) cc_final: 0.7225 (p) REVERT: P 53 LYS cc_start: 0.6690 (ttmt) cc_final: 0.5690 (ttpp) REVERT: P 71 LYS cc_start: 0.6177 (ttpp) cc_final: 0.5933 (ttpp) REVERT: Q 27 GLU cc_start: 0.5927 (mm-30) cc_final: 0.5338 (mm-30) REVERT: Q 53 LYS cc_start: 0.6724 (ttmt) cc_final: 0.5723 (ttpp) REVERT: R 53 LYS cc_start: 0.6719 (ttmt) cc_final: 0.5560 (ttpp) REVERT: S 14 GLN cc_start: 0.6441 (mm-40) cc_final: 0.5411 (pt0) REVERT: S 53 LYS cc_start: 0.6719 (ttmt) cc_final: 0.5659 (ttpp) REVERT: T 53 LYS cc_start: 0.6708 (ttmt) cc_final: 0.5737 (ttpp) REVERT: U 27 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6762 (mm-30) REVERT: U 53 LYS cc_start: 0.6726 (ttmt) cc_final: 0.5681 (ttpp) REVERT: U 140 GLU cc_start: 0.6304 (mm-30) cc_final: 0.5126 (mp0) REVERT: V 53 LYS cc_start: 0.6754 (ttmt) cc_final: 0.5685 (ttpp) REVERT: W 53 LYS cc_start: 0.6712 (ttmt) cc_final: 0.5741 (ttpp) REVERT: X 53 LYS cc_start: 0.6708 (ttmt) cc_final: 0.5713 (ttpp) REVERT: X 136 TYR cc_start: 0.7766 (m-80) cc_final: 0.7528 (m-80) REVERT: X 140 GLU cc_start: 0.6341 (mm-30) cc_final: 0.5182 (mp0) outliers start: 73 outliers final: 50 residues processed: 660 average time/residue: 2.9737 time to fit residues: 2314.9882 Evaluate side-chains 647 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 596 time to evaluate : 4.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 167 GLU Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain L residue 113 SER Chi-restraints excluded: chain L residue 167 GLU Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 167 GLU Chi-restraints excluded: chain N residue 68 LYS Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain O residue 167 GLU Chi-restraints excluded: chain P residue 94 GLU Chi-restraints excluded: chain P residue 167 GLU Chi-restraints excluded: chain Q residue 113 SER Chi-restraints excluded: chain Q residue 167 GLU Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 167 GLU Chi-restraints excluded: chain S residue 167 GLU Chi-restraints excluded: chain T residue 167 GLU Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain U residue 167 GLU Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 167 GLU Chi-restraints excluded: chain W residue 113 SER Chi-restraints excluded: chain W residue 167 GLU Chi-restraints excluded: chain X residue 167 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 5.9990 chunk 309 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 208 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 319 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 238 optimal weight: 5.9990 chunk 370 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 GLN C 7 GLN E 7 GLN E 10 GLN G 111 ASN H 7 GLN I 7 GLN J 7 GLN K 14 GLN O 7 GLN ** O 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 14 GLN P 98 ASN Q 7 GLN Q 98 ASN R 7 GLN S 7 GLN S 111 ASN T 7 GLN ** U 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.0719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 34512 Z= 0.408 Angle : 0.635 7.022 46416 Z= 0.344 Chirality : 0.040 0.168 4848 Planarity : 0.005 0.059 6096 Dihedral : 7.325 55.743 4627 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.66 % Allowed : 17.85 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 2.99 (0.13), residues: 4080 helix: 2.54 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.23 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP A 93 HIS 0.006 0.001 HIS E 173 PHE 0.021 0.003 PHE N 41 TYR 0.022 0.003 TYR I 137 ARG 0.005 0.001 ARG Q 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 699 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 602 time to evaluate : 4.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6115 (mm-30) cc_final: 0.5423 (mm-30) REVERT: A 53 LYS cc_start: 0.6750 (ttmt) cc_final: 0.5660 (ttpp) REVERT: A 135 THR cc_start: 0.7567 (t) cc_final: 0.7276 (m) REVERT: A 140 GLU cc_start: 0.6389 (mm-30) cc_final: 0.5194 (mp0) REVERT: B 14 GLN cc_start: 0.6343 (OUTLIER) cc_final: 0.5675 (mp10) REVERT: B 53 LYS cc_start: 0.6743 (ttmt) cc_final: 0.5678 (ttpp) REVERT: B 140 GLU cc_start: 0.6387 (mm-30) cc_final: 0.5178 (mp0) REVERT: C 53 LYS cc_start: 0.6734 (ttmt) cc_final: 0.5671 (ttpp) REVERT: D 53 LYS cc_start: 0.6742 (ttmt) cc_final: 0.5671 (ttpp) REVERT: E 27 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6616 (mm-30) REVERT: E 53 LYS cc_start: 0.6749 (ttmt) cc_final: 0.5691 (ttpp) REVERT: E 63 ARG cc_start: 0.6581 (OUTLIER) cc_final: 0.6326 (tmm160) REVERT: F 53 LYS cc_start: 0.6727 (ttmt) cc_final: 0.5658 (ttpp) REVERT: I 53 LYS cc_start: 0.6720 (ttmt) cc_final: 0.5560 (ttpp) REVERT: J 27 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6674 (mm-30) REVERT: J 53 LYS cc_start: 0.6706 (ttmt) cc_final: 0.5645 (ttpp) REVERT: K 53 LYS cc_start: 0.6736 (ttmt) cc_final: 0.5661 (ttpp) REVERT: L 53 LYS cc_start: 0.6756 (ttmt) cc_final: 0.5682 (ttpp) REVERT: L 67 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6877 (mt-10) REVERT: M 17 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6668 (tt0) REVERT: M 53 LYS cc_start: 0.6726 (ttmt) cc_final: 0.5648 (ttpp) REVERT: N 53 LYS cc_start: 0.6719 (ttmt) cc_final: 0.5641 (ttpp) REVERT: O 27 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6532 (mm-30) REVERT: O 53 LYS cc_start: 0.6722 (ttmt) cc_final: 0.5653 (ttpp) REVERT: O 63 ARG cc_start: 0.6637 (OUTLIER) cc_final: 0.6415 (tmm160) REVERT: P 14 GLN cc_start: 0.6236 (OUTLIER) cc_final: 0.5376 (pt0) REVERT: P 27 GLU cc_start: 0.6171 (mm-30) cc_final: 0.5434 (mm-30) REVERT: P 53 LYS cc_start: 0.6725 (ttmt) cc_final: 0.5644 (ttpp) REVERT: Q 27 GLU cc_start: 0.6128 (mm-30) cc_final: 0.5474 (mm-30) REVERT: Q 53 LYS cc_start: 0.6718 (ttmt) cc_final: 0.5649 (ttpp) REVERT: R 53 LYS cc_start: 0.6710 (ttmt) cc_final: 0.5534 (ttpp) REVERT: S 27 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6622 (mm-30) REVERT: S 53 LYS cc_start: 0.6712 (ttmt) cc_final: 0.5562 (ttpp) REVERT: T 53 LYS cc_start: 0.6753 (ttmt) cc_final: 0.5680 (ttpp) REVERT: U 27 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6937 (mm-30) REVERT: U 53 LYS cc_start: 0.6752 (ttmt) cc_final: 0.5676 (ttpp) REVERT: U 140 GLU cc_start: 0.6357 (mm-30) cc_final: 0.5173 (mp0) REVERT: V 53 LYS cc_start: 0.6742 (ttmt) cc_final: 0.5583 (ttpp) REVERT: W 53 LYS cc_start: 0.6747 (ttmt) cc_final: 0.5682 (ttpp) REVERT: X 53 LYS cc_start: 0.6695 (ttmt) cc_final: 0.5626 (ttpp) REVERT: X 140 GLU cc_start: 0.6401 (mm-30) cc_final: 0.5217 (mp0) outliers start: 97 outliers final: 61 residues processed: 644 average time/residue: 3.0525 time to fit residues: 2306.8110 Evaluate side-chains 637 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 565 time to evaluate : 4.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 27 GLU Chi-restraints excluded: chain O residue 63 ARG Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 94 GLU Chi-restraints excluded: chain P residue 113 SER Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 94 GLU Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 27 GLU Chi-restraints excluded: chain S residue 113 SER Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain U residue 27 GLU Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain U residue 143 LYS Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 113 SER Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 165 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 4.9990 chunk 114 optimal weight: 0.4980 chunk 308 optimal weight: 3.9990 chunk 252 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 371 optimal weight: 3.9990 chunk 400 optimal weight: 4.9990 chunk 330 optimal weight: 4.9990 chunk 368 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 297 optimal weight: 2.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN F 7 GLN G 7 GLN K 7 GLN N 7 GLN ** O 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 7 GLN U 7 GLN V 7 GLN W 7 GLN X 7 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 34512 Z= 0.295 Angle : 0.567 6.357 46416 Z= 0.306 Chirality : 0.036 0.141 4848 Planarity : 0.004 0.046 6096 Dihedral : 5.093 56.561 4530 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.19 % Allowed : 18.45 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.31 (0.13), residues: 4080 helix: 2.79 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.21 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP R 93 HIS 0.004 0.001 HIS T 128 PHE 0.017 0.002 PHE N 41 TYR 0.019 0.002 TYR I 137 ARG 0.006 0.000 ARG S 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 687 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 607 time to evaluate : 4.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.5998 (mm-30) cc_final: 0.5360 (mm-30) REVERT: A 53 LYS cc_start: 0.6746 (ttmt) cc_final: 0.5707 (ttpp) REVERT: A 64 GLU cc_start: 0.6107 (mt-10) cc_final: 0.5849 (mt-10) REVERT: A 140 GLU cc_start: 0.6397 (mm-30) cc_final: 0.5208 (mp0) REVERT: B 14 GLN cc_start: 0.6364 (OUTLIER) cc_final: 0.5730 (mp10) REVERT: B 15 ASP cc_start: 0.6909 (p0) cc_final: 0.6115 (m-30) REVERT: B 53 LYS cc_start: 0.6713 (ttmt) cc_final: 0.5564 (ttpp) REVERT: B 68 LYS cc_start: 0.6945 (OUTLIER) cc_final: 0.6532 (tttp) REVERT: B 140 GLU cc_start: 0.6389 (mm-30) cc_final: 0.5187 (mp0) REVERT: C 53 LYS cc_start: 0.6769 (ttmt) cc_final: 0.5702 (ttpp) REVERT: C 63 ARG cc_start: 0.6518 (tmm160) cc_final: 0.5659 (tmm160) REVERT: D 53 LYS cc_start: 0.6737 (ttmt) cc_final: 0.5706 (ttpp) REVERT: D 140 GLU cc_start: 0.6413 (mm-30) cc_final: 0.5188 (mp0) REVERT: E 27 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6406 (mt-10) REVERT: E 53 LYS cc_start: 0.6740 (ttmt) cc_final: 0.5681 (ttpp) REVERT: E 68 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6583 (tttp) REVERT: F 53 LYS cc_start: 0.6773 (ttmt) cc_final: 0.5733 (ttpp) REVERT: G 140 GLU cc_start: 0.6381 (mm-30) cc_final: 0.5189 (mp0) REVERT: I 53 LYS cc_start: 0.6738 (ttmt) cc_final: 0.5578 (ttpp) REVERT: J 27 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6508 (mm-30) REVERT: J 53 LYS cc_start: 0.6754 (ttmt) cc_final: 0.5719 (ttpp) REVERT: K 53 LYS cc_start: 0.6778 (ttmt) cc_final: 0.5737 (ttpp) REVERT: K 63 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.6246 (tmm160) REVERT: L 17 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.6456 (tt0) REVERT: L 53 LYS cc_start: 0.6773 (ttmt) cc_final: 0.5726 (ttpp) REVERT: L 67 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6856 (mt-10) REVERT: M 17 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6620 (tt0) REVERT: M 53 LYS cc_start: 0.6769 (ttmt) cc_final: 0.5719 (ttpp) REVERT: M 140 GLU cc_start: 0.6387 (mm-30) cc_final: 0.5190 (mp0) REVERT: N 53 LYS cc_start: 0.6742 (ttmt) cc_final: 0.5585 (ttpp) REVERT: O 27 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6443 (mm-30) REVERT: O 53 LYS cc_start: 0.6783 (ttmt) cc_final: 0.5744 (ttpp) REVERT: P 14 GLN cc_start: 0.5965 (mp10) cc_final: 0.5167 (pt0) REVERT: P 27 GLU cc_start: 0.6110 (mm-30) cc_final: 0.5452 (mm-30) REVERT: P 53 LYS cc_start: 0.6755 (ttmt) cc_final: 0.5701 (ttpp) REVERT: P 140 GLU cc_start: 0.6407 (mm-30) cc_final: 0.5192 (mp0) REVERT: Q 27 GLU cc_start: 0.6025 (mm-30) cc_final: 0.5420 (mm-30) REVERT: Q 53 LYS cc_start: 0.6727 (ttmt) cc_final: 0.5702 (ttpp) REVERT: Q 64 GLU cc_start: 0.5996 (mt-10) cc_final: 0.5771 (mt-10) REVERT: Q 140 GLU cc_start: 0.6402 (mm-30) cc_final: 0.5215 (mp0) REVERT: R 53 LYS cc_start: 0.6732 (ttmt) cc_final: 0.5553 (ttpp) REVERT: S 27 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6562 (mm-30) REVERT: S 53 LYS cc_start: 0.6718 (ttmt) cc_final: 0.5561 (ttpp) REVERT: T 17 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6485 (tt0) REVERT: T 53 LYS cc_start: 0.6780 (ttmt) cc_final: 0.5737 (ttpp) REVERT: U 27 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6602 (mt-10) REVERT: U 53 LYS cc_start: 0.6726 (ttmt) cc_final: 0.5693 (ttpp) REVERT: U 140 GLU cc_start: 0.6393 (mm-30) cc_final: 0.5204 (mp0) REVERT: V 53 LYS cc_start: 0.6766 (ttmt) cc_final: 0.5606 (ttpp) REVERT: W 53 LYS cc_start: 0.6796 (ttmt) cc_final: 0.5745 (ttpp) REVERT: W 64 GLU cc_start: 0.6135 (mt-10) cc_final: 0.5889 (mt-10) REVERT: W 71 LYS cc_start: 0.6039 (ttpp) cc_final: 0.5837 (ttpp) REVERT: W 140 GLU cc_start: 0.6329 (mm-30) cc_final: 0.5163 (mp0) REVERT: X 53 LYS cc_start: 0.6737 (ttmt) cc_final: 0.5662 (ttpp) REVERT: X 140 GLU cc_start: 0.6427 (mm-30) cc_final: 0.5227 (mp0) outliers start: 80 outliers final: 43 residues processed: 643 average time/residue: 3.0002 time to fit residues: 2267.6490 Evaluate side-chains 634 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 578 time to evaluate : 4.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain L residue 113 SER Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 27 GLU Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 94 GLU Chi-restraints excluded: chain P residue 113 SER Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain P residue 167 GLU Chi-restraints excluded: chain Q residue 94 GLU Chi-restraints excluded: chain Q residue 113 SER Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 27 GLU Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 17 GLU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain U residue 27 GLU Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain U residue 143 LYS Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 113 SER Chi-restraints excluded: chain X residue 165 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 3.9990 chunk 279 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 chunk 372 optimal weight: 3.9990 chunk 394 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 353 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 98 ASN ** O 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 34512 Z= 0.345 Angle : 0.585 6.828 46416 Z= 0.317 Chirality : 0.038 0.133 4848 Planarity : 0.004 0.048 6096 Dihedral : 5.098 59.408 4524 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.04 % Allowed : 17.54 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.13), residues: 4080 helix: 2.70 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.30 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.004 TRP A 93 HIS 0.004 0.001 HIS O 13 PHE 0.018 0.003 PHE N 41 TYR 0.017 0.002 TYR L 137 ARG 0.004 0.001 ARG L 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 700 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 589 time to evaluate : 4.182 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.5995 (mm-30) cc_final: 0.5314 (mm-30) REVERT: A 53 LYS cc_start: 0.6761 (ttmt) cc_final: 0.5587 (ttpp) REVERT: A 64 GLU cc_start: 0.6075 (mt-10) cc_final: 0.5807 (mt-10) REVERT: A 140 GLU cc_start: 0.6395 (mm-30) cc_final: 0.5203 (mp0) REVERT: B 14 GLN cc_start: 0.6352 (OUTLIER) cc_final: 0.5734 (mp10) REVERT: B 15 ASP cc_start: 0.6880 (p0) cc_final: 0.6111 (m-30) REVERT: B 53 LYS cc_start: 0.6663 (ttmt) cc_final: 0.5514 (ttpp) REVERT: B 140 GLU cc_start: 0.6412 (mm-30) cc_final: 0.5218 (mp0) REVERT: C 53 LYS cc_start: 0.6777 (ttmt) cc_final: 0.5624 (ttpp) REVERT: C 64 GLU cc_start: 0.6089 (mt-10) cc_final: 0.5811 (mt-10) REVERT: D 53 LYS cc_start: 0.6780 (ttmt) cc_final: 0.5733 (ttpp) REVERT: E 27 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6472 (mt-10) REVERT: E 53 LYS cc_start: 0.6784 (ttmt) cc_final: 0.5734 (ttpp) REVERT: E 63 ARG cc_start: 0.6625 (OUTLIER) cc_final: 0.6377 (tmm160) REVERT: F 53 LYS cc_start: 0.6782 (ttmt) cc_final: 0.5620 (ttpp) REVERT: I 53 LYS cc_start: 0.6737 (ttmt) cc_final: 0.5576 (ttpp) REVERT: J 27 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6523 (mm-30) REVERT: J 53 LYS cc_start: 0.6762 (ttmt) cc_final: 0.5604 (ttpp) REVERT: K 53 LYS cc_start: 0.6786 (ttmt) cc_final: 0.5619 (ttpp) REVERT: K 63 ARG cc_start: 0.6639 (OUTLIER) cc_final: 0.6295 (tmm160) REVERT: L 53 LYS cc_start: 0.6807 (ttmt) cc_final: 0.5632 (ttpp) REVERT: L 67 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6891 (mt-10) REVERT: M 53 LYS cc_start: 0.6796 (ttmt) cc_final: 0.5618 (ttpp) REVERT: N 53 LYS cc_start: 0.6753 (ttmt) cc_final: 0.5584 (ttpp) REVERT: O 27 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6475 (mm-30) REVERT: O 53 LYS cc_start: 0.6802 (ttmt) cc_final: 0.5635 (ttpp) REVERT: P 14 GLN cc_start: 0.6120 (mp10) cc_final: 0.5428 (pt0) REVERT: P 27 GLU cc_start: 0.6112 (mm-30) cc_final: 0.5423 (mm-30) REVERT: P 53 LYS cc_start: 0.6774 (ttmt) cc_final: 0.5599 (ttpp) REVERT: Q 27 GLU cc_start: 0.6107 (mm-30) cc_final: 0.5490 (mm-30) REVERT: Q 53 LYS cc_start: 0.6759 (ttmt) cc_final: 0.5604 (ttpp) REVERT: Q 64 GLU cc_start: 0.6027 (mt-10) cc_final: 0.5780 (mt-10) REVERT: R 53 LYS cc_start: 0.6759 (ttmt) cc_final: 0.5573 (ttpp) REVERT: S 27 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6591 (mm-30) REVERT: S 53 LYS cc_start: 0.6727 (ttmt) cc_final: 0.5572 (ttpp) REVERT: T 53 LYS cc_start: 0.6801 (ttmt) cc_final: 0.5741 (ttpp) REVERT: U 27 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6544 (mt-10) REVERT: U 53 LYS cc_start: 0.6773 (ttmt) cc_final: 0.5605 (ttpp) REVERT: U 140 GLU cc_start: 0.6402 (mm-30) cc_final: 0.5203 (mp0) REVERT: V 53 LYS cc_start: 0.6764 (ttmt) cc_final: 0.5599 (ttpp) REVERT: W 53 LYS cc_start: 0.6816 (ttmt) cc_final: 0.5646 (ttpp) REVERT: W 71 LYS cc_start: 0.6177 (ttpp) cc_final: 0.5969 (ttpp) REVERT: X 53 LYS cc_start: 0.6747 (ttmt) cc_final: 0.5586 (ttpp) REVERT: X 140 GLU cc_start: 0.6429 (mm-30) cc_final: 0.5234 (mp0) outliers start: 111 outliers final: 68 residues processed: 656 average time/residue: 3.0308 time to fit residues: 2354.3738 Evaluate side-chains 649 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 572 time to evaluate : 4.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain L residue 113 SER Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 27 GLU Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 94 GLU Chi-restraints excluded: chain P residue 113 SER Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain P residue 167 GLU Chi-restraints excluded: chain Q residue 94 GLU Chi-restraints excluded: chain Q residue 113 SER Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 167 GLU Chi-restraints excluded: chain S residue 27 GLU Chi-restraints excluded: chain S residue 113 SER Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain U residue 27 GLU Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain U residue 143 LYS Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 113 SER Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 113 SER Chi-restraints excluded: chain X residue 165 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 293 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 336 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 353 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 ASN ** O 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 34512 Z= 0.400 Angle : 0.611 5.985 46416 Z= 0.331 Chirality : 0.039 0.143 4848 Planarity : 0.005 0.037 6096 Dihedral : 5.230 57.970 4524 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.59 % Allowed : 16.80 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 2.97 (0.13), residues: 4080 helix: 2.56 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.41 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP R 93 HIS 0.004 0.001 HIS O 128 PHE 0.019 0.003 PHE N 41 TYR 0.018 0.002 TYR L 137 ARG 0.005 0.001 ARG L 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 725 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 594 time to evaluate : 4.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6019 (mm-30) cc_final: 0.5370 (mm-30) REVERT: A 53 LYS cc_start: 0.6713 (ttmt) cc_final: 0.5548 (ttpp) REVERT: A 64 GLU cc_start: 0.6094 (mt-10) cc_final: 0.5851 (mt-10) REVERT: A 135 THR cc_start: 0.7415 (t) cc_final: 0.7179 (m) REVERT: A 140 GLU cc_start: 0.6377 (mm-30) cc_final: 0.5197 (mp0) REVERT: B 14 GLN cc_start: 0.6371 (OUTLIER) cc_final: 0.5766 (mp10) REVERT: B 15 ASP cc_start: 0.6876 (p0) cc_final: 0.6184 (m-30) REVERT: B 53 LYS cc_start: 0.6663 (ttmt) cc_final: 0.5499 (ttpp) REVERT: B 140 GLU cc_start: 0.6385 (mm-30) cc_final: 0.5212 (mp0) REVERT: C 53 LYS cc_start: 0.6747 (ttmt) cc_final: 0.5579 (ttpp) REVERT: C 63 ARG cc_start: 0.6573 (OUTLIER) cc_final: 0.6117 (tmm160) REVERT: C 64 GLU cc_start: 0.6062 (mt-10) cc_final: 0.5788 (mt-10) REVERT: D 53 LYS cc_start: 0.6750 (ttmt) cc_final: 0.5583 (ttpp) REVERT: D 64 GLU cc_start: 0.6061 (mt-10) cc_final: 0.5830 (mt-10) REVERT: D 140 GLU cc_start: 0.6422 (mm-30) cc_final: 0.5225 (mp0) REVERT: E 27 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6657 (mm-30) REVERT: E 53 LYS cc_start: 0.6781 (ttmt) cc_final: 0.5612 (ttpp) REVERT: F 53 LYS cc_start: 0.6747 (ttmt) cc_final: 0.5585 (ttpp) REVERT: G 140 GLU cc_start: 0.6404 (mm-30) cc_final: 0.5203 (mp0) REVERT: I 53 LYS cc_start: 0.6693 (ttmt) cc_final: 0.5535 (ttpp) REVERT: J 27 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6495 (mm-30) REVERT: J 53 LYS cc_start: 0.6785 (ttmt) cc_final: 0.5615 (ttpp) REVERT: J 135 THR cc_start: 0.7461 (t) cc_final: 0.7208 (m) REVERT: K 53 LYS cc_start: 0.6752 (ttmt) cc_final: 0.5589 (ttpp) REVERT: L 53 LYS cc_start: 0.6805 (ttmt) cc_final: 0.5619 (ttpp) REVERT: L 67 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6968 (mt-10) REVERT: M 53 LYS cc_start: 0.6740 (ttmt) cc_final: 0.5573 (ttpp) REVERT: M 140 GLU cc_start: 0.6408 (mm-30) cc_final: 0.5203 (mp0) REVERT: N 53 LYS cc_start: 0.6703 (ttmt) cc_final: 0.5545 (ttpp) REVERT: N 135 THR cc_start: 0.7487 (t) cc_final: 0.7238 (m) REVERT: O 27 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6567 (mm-30) REVERT: O 53 LYS cc_start: 0.6757 (ttmt) cc_final: 0.5593 (ttpp) REVERT: O 63 ARG cc_start: 0.6614 (OUTLIER) cc_final: 0.6339 (tmm160) REVERT: O 135 THR cc_start: 0.7454 (t) cc_final: 0.7213 (m) REVERT: P 14 GLN cc_start: 0.6149 (OUTLIER) cc_final: 0.5475 (pt0) REVERT: P 27 GLU cc_start: 0.6118 (mm-30) cc_final: 0.5456 (mm-30) REVERT: P 53 LYS cc_start: 0.6743 (ttmt) cc_final: 0.5569 (ttpp) REVERT: Q 27 GLU cc_start: 0.6097 (mm-30) cc_final: 0.5442 (mm-30) REVERT: Q 53 LYS cc_start: 0.6725 (ttmt) cc_final: 0.5566 (ttpp) REVERT: Q 64 GLU cc_start: 0.6098 (mt-10) cc_final: 0.5875 (mt-10) REVERT: R 53 LYS cc_start: 0.6707 (ttmt) cc_final: 0.5526 (ttpp) REVERT: R 71 LYS cc_start: 0.6145 (OUTLIER) cc_final: 0.5764 (ttpp) REVERT: S 27 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6590 (mm-30) REVERT: S 53 LYS cc_start: 0.6680 (ttmt) cc_final: 0.5536 (ttpp) REVERT: T 53 LYS cc_start: 0.6809 (ttmt) cc_final: 0.5630 (ttpp) REVERT: U 27 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6777 (mm-30) REVERT: U 53 LYS cc_start: 0.6724 (ttmt) cc_final: 0.5564 (ttpp) REVERT: V 53 LYS cc_start: 0.6720 (ttmt) cc_final: 0.5563 (ttpp) REVERT: W 53 LYS cc_start: 0.6756 (ttmt) cc_final: 0.5589 (ttpp) REVERT: X 27 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.5667 (mt-10) REVERT: X 53 LYS cc_start: 0.6709 (ttmt) cc_final: 0.5549 (ttpp) REVERT: X 140 GLU cc_start: 0.6417 (mm-30) cc_final: 0.5219 (mp0) outliers start: 131 outliers final: 83 residues processed: 665 average time/residue: 2.9978 time to fit residues: 2347.7923 Evaluate side-chains 674 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 579 time to evaluate : 4.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain L residue 113 SER Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 68 LYS Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 27 GLU Chi-restraints excluded: chain O residue 63 ARG Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 94 GLU Chi-restraints excluded: chain P residue 113 SER Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain P residue 167 GLU Chi-restraints excluded: chain Q residue 94 GLU Chi-restraints excluded: chain Q residue 113 SER Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 68 LYS Chi-restraints excluded: chain R residue 71 LYS Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 167 GLU Chi-restraints excluded: chain S residue 27 GLU Chi-restraints excluded: chain S residue 113 SER Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain U residue 27 GLU Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain U residue 143 LYS Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 113 SER Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 27 GLU Chi-restraints excluded: chain X residue 113 SER Chi-restraints excluded: chain X residue 165 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 2.9990 chunk 355 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 231 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 394 optimal weight: 0.8980 chunk 327 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 7 GLN M 7 GLN M 98 ASN ** O 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 34512 Z= 0.250 Angle : 0.534 6.098 46416 Z= 0.287 Chirality : 0.034 0.123 4848 Planarity : 0.003 0.030 6096 Dihedral : 4.975 59.825 4524 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.11 % Allowed : 17.71 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.59 (0.13), residues: 4080 helix: 3.00 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.18 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP A 93 HIS 0.003 0.001 HIS T 128 PHE 0.015 0.002 PHE E 41 TYR 0.015 0.002 TYR I 137 ARG 0.005 0.000 ARG V 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 667 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 590 time to evaluate : 4.690 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: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.5966 (mm-30) cc_final: 0.5341 (mm-30) REVERT: A 53 LYS cc_start: 0.6718 (ttmt) cc_final: 0.5670 (ttpp) REVERT: A 64 GLU cc_start: 0.6107 (mt-10) cc_final: 0.5877 (mt-10) REVERT: A 140 GLU cc_start: 0.6410 (mm-30) cc_final: 0.5212 (mp0) REVERT: B 15 ASP cc_start: 0.6830 (p0) cc_final: 0.6174 (m-30) REVERT: B 53 LYS cc_start: 0.6766 (ttmt) cc_final: 0.5633 (ttpp) REVERT: B 140 GLU cc_start: 0.6428 (mm-30) cc_final: 0.5231 (mp0) REVERT: C 53 LYS cc_start: 0.6751 (ttmt) cc_final: 0.5601 (ttpp) REVERT: C 63 ARG cc_start: 0.6474 (OUTLIER) cc_final: 0.5986 (tmm160) REVERT: D 53 LYS cc_start: 0.6681 (ttmt) cc_final: 0.5525 (ttpp) REVERT: D 140 GLU cc_start: 0.6410 (mm-30) cc_final: 0.5206 (mp0) REVERT: E 27 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6417 (mt-10) REVERT: E 53 LYS cc_start: 0.6747 (ttmt) cc_final: 0.5709 (ttpp) REVERT: F 17 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6524 (tt0) REVERT: F 53 LYS cc_start: 0.6756 (ttmt) cc_final: 0.5606 (ttpp) REVERT: F 64 GLU cc_start: 0.6112 (mt-10) cc_final: 0.5892 (mt-10) REVERT: G 17 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6471 (tt0) REVERT: G 140 GLU cc_start: 0.6421 (mm-30) cc_final: 0.5156 (mp0) REVERT: I 17 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6578 (tt0) REVERT: I 53 LYS cc_start: 0.6718 (ttmt) cc_final: 0.5572 (ttpp) REVERT: I 140 GLU cc_start: 0.6409 (mm-30) cc_final: 0.5198 (mp0) REVERT: J 27 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6494 (mm-30) REVERT: J 53 LYS cc_start: 0.6722 (ttmt) cc_final: 0.5684 (ttpp) REVERT: J 63 ARG cc_start: 0.6648 (OUTLIER) cc_final: 0.6183 (tmm160) REVERT: K 53 LYS cc_start: 0.6747 (ttmt) cc_final: 0.5596 (ttpp) REVERT: L 17 GLU cc_start: 0.6663 (OUTLIER) cc_final: 0.6394 (tt0) REVERT: L 53 LYS cc_start: 0.6659 (ttmt) cc_final: 0.5494 (ttpp) REVERT: L 67 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6859 (mt-10) REVERT: M 17 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6495 (tt0) REVERT: M 53 LYS cc_start: 0.6658 (ttmt) cc_final: 0.5500 (ttpp) REVERT: M 140 GLU cc_start: 0.6395 (mm-30) cc_final: 0.5192 (mp0) REVERT: N 53 LYS cc_start: 0.6724 (ttmt) cc_final: 0.5583 (ttpp) REVERT: N 71 LYS cc_start: 0.6148 (ttpp) cc_final: 0.5931 (ttpp) REVERT: O 27 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.5977 (mt-10) REVERT: O 53 LYS cc_start: 0.6751 (ttmt) cc_final: 0.5601 (ttpp) REVERT: O 71 LYS cc_start: 0.6083 (ttpp) cc_final: 0.5832 (ttpp) REVERT: O 119 LYS cc_start: 0.6531 (tttt) cc_final: 0.5612 (ttpp) REVERT: P 27 GLU cc_start: 0.6013 (mm-30) cc_final: 0.5369 (mm-30) REVERT: P 53 LYS cc_start: 0.6651 (ttmt) cc_final: 0.5490 (ttpp) REVERT: P 140 GLU cc_start: 0.6395 (mm-30) cc_final: 0.5213 (mp0) REVERT: Q 27 GLU cc_start: 0.5996 (mm-30) cc_final: 0.5426 (mm-30) REVERT: Q 53 LYS cc_start: 0.6735 (ttmt) cc_final: 0.5590 (ttpp) REVERT: Q 140 GLU cc_start: 0.6391 (mm-30) cc_final: 0.5183 (mp0) REVERT: R 53 LYS cc_start: 0.6720 (ttmt) cc_final: 0.5555 (ttpp) REVERT: S 27 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6572 (mm-30) REVERT: S 53 LYS cc_start: 0.6702 (ttmt) cc_final: 0.5565 (ttpp) REVERT: T 17 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6529 (tt0) REVERT: T 53 LYS cc_start: 0.6744 (ttmt) cc_final: 0.5706 (ttpp) REVERT: U 27 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6507 (mt-10) REVERT: U 53 LYS cc_start: 0.6734 (ttmt) cc_final: 0.5585 (ttpp) REVERT: U 140 GLU cc_start: 0.6395 (mm-30) cc_final: 0.5204 (mp0) REVERT: V 53 LYS cc_start: 0.6735 (ttmt) cc_final: 0.5590 (ttpp) REVERT: V 140 GLU cc_start: 0.6396 (mm-30) cc_final: 0.5202 (mp0) REVERT: W 17 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6521 (tt0) REVERT: W 53 LYS cc_start: 0.6753 (ttmt) cc_final: 0.5603 (ttpp) REVERT: W 140 GLU cc_start: 0.6380 (mm-30) cc_final: 0.5196 (mp0) REVERT: X 53 LYS cc_start: 0.6726 (ttmt) cc_final: 0.5574 (ttpp) REVERT: X 140 GLU cc_start: 0.6421 (mm-30) cc_final: 0.5231 (mp0) outliers start: 77 outliers final: 50 residues processed: 620 average time/residue: 2.9641 time to fit residues: 2163.8860 Evaluate side-chains 654 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 589 time to evaluate : 4.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain L residue 113 SER Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 27 GLU Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 94 GLU Chi-restraints excluded: chain P residue 113 SER Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 94 GLU Chi-restraints excluded: chain Q residue 113 SER Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 27 GLU Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 17 GLU Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain U residue 27 GLU Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 113 SER Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 165 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 224 optimal weight: 0.7980 chunk 288 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 332 optimal weight: 5.9990 chunk 220 optimal weight: 0.8980 chunk 393 optimal weight: 3.9990 chunk 246 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 98 ASN O 10 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 34512 Z= 0.222 Angle : 0.519 5.803 46416 Z= 0.278 Chirality : 0.033 0.120 4848 Planarity : 0.003 0.025 6096 Dihedral : 4.841 59.643 4524 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.86 % Allowed : 18.04 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.91 (0.13), residues: 4080 helix: 3.22 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.04 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP A 93 HIS 0.003 0.001 HIS P 128 PHE 0.014 0.002 PHE E 41 TYR 0.013 0.001 TYR G 137 ARG 0.007 0.000 ARG T 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 661 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 593 time to evaluate : 4.093 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.5999 (mm-30) cc_final: 0.5412 (mm-30) REVERT: A 53 LYS cc_start: 0.6704 (ttmt) cc_final: 0.5679 (ttpp) REVERT: A 64 GLU cc_start: 0.6102 (mt-10) cc_final: 0.5870 (mt-10) REVERT: A 119 LYS cc_start: 0.5688 (mmtm) cc_final: 0.5413 (ttmt) REVERT: A 140 GLU cc_start: 0.6412 (mm-30) cc_final: 0.5176 (mp0) REVERT: B 15 ASP cc_start: 0.6876 (p0) cc_final: 0.6264 (m-30) REVERT: B 53 LYS cc_start: 0.6702 (ttmt) cc_final: 0.5584 (ttpp) REVERT: B 63 ARG cc_start: 0.6574 (tmm160) cc_final: 0.6210 (tmm160) REVERT: B 64 GLU cc_start: 0.6089 (mt-10) cc_final: 0.5852 (mt-10) REVERT: B 71 LYS cc_start: 0.6038 (ttpp) cc_final: 0.5832 (ttpp) REVERT: B 140 GLU cc_start: 0.6453 (mm-30) cc_final: 0.5166 (mp0) REVERT: C 53 LYS cc_start: 0.6745 (ttmt) cc_final: 0.5613 (ttpp) REVERT: C 143 LYS cc_start: 0.6055 (ttpp) cc_final: 0.5235 (mttm) REVERT: D 53 LYS cc_start: 0.6647 (ttmt) cc_final: 0.5629 (ttpp) REVERT: D 140 GLU cc_start: 0.6452 (mm-30) cc_final: 0.5187 (mp0) REVERT: E 27 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6552 (mm-30) REVERT: E 53 LYS cc_start: 0.6712 (ttmt) cc_final: 0.5704 (ttpp) REVERT: E 71 LYS cc_start: 0.6044 (ttpp) cc_final: 0.5820 (ttpp) REVERT: F 17 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6388 (tt0) REVERT: F 53 LYS cc_start: 0.6725 (ttmt) cc_final: 0.5707 (ttpp) REVERT: G 17 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6473 (tt0) REVERT: G 140 GLU cc_start: 0.6415 (mm-30) cc_final: 0.5160 (mp0) REVERT: I 17 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6551 (tt0) REVERT: I 53 LYS cc_start: 0.6732 (ttmt) cc_final: 0.5607 (ttpp) REVERT: I 140 GLU cc_start: 0.6438 (mm-30) cc_final: 0.5214 (mp0) REVERT: J 27 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6489 (mm-30) REVERT: J 53 LYS cc_start: 0.6687 (ttmt) cc_final: 0.5668 (ttpp) REVERT: K 53 LYS cc_start: 0.6742 (ttmt) cc_final: 0.5718 (ttpp) REVERT: K 71 LYS cc_start: 0.6010 (ttpp) cc_final: 0.5750 (ttpp) REVERT: L 17 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6385 (tt0) REVERT: L 53 LYS cc_start: 0.6660 (ttmt) cc_final: 0.5634 (ttpp) REVERT: L 67 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6806 (mt-10) REVERT: M 17 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6522 (tt0) REVERT: M 53 LYS cc_start: 0.6601 (ttmt) cc_final: 0.5465 (ttpp) REVERT: M 140 GLU cc_start: 0.6438 (mm-30) cc_final: 0.5174 (mp0) REVERT: N 53 LYS cc_start: 0.6684 (ttmt) cc_final: 0.5568 (ttpp) REVERT: N 71 LYS cc_start: 0.6064 (ttpp) cc_final: 0.5854 (ttpp) REVERT: O 27 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6419 (mm-30) REVERT: O 53 LYS cc_start: 0.6738 (ttmt) cc_final: 0.5710 (ttpp) REVERT: O 71 LYS cc_start: 0.6004 (ttpp) cc_final: 0.5759 (ttpp) REVERT: O 119 LYS cc_start: 0.6515 (tttt) cc_final: 0.5590 (ttpp) REVERT: P 27 GLU cc_start: 0.6060 (mm-30) cc_final: 0.5445 (mm-30) REVERT: P 53 LYS cc_start: 0.6609 (ttmt) cc_final: 0.5594 (ttpp) REVERT: P 140 GLU cc_start: 0.6394 (mm-30) cc_final: 0.5203 (mp0) REVERT: Q 27 GLU cc_start: 0.6006 (mm-30) cc_final: 0.5403 (mm-30) REVERT: Q 53 LYS cc_start: 0.6696 (ttmt) cc_final: 0.5687 (ttpp) REVERT: Q 140 GLU cc_start: 0.6456 (mm-30) cc_final: 0.5237 (mp0) REVERT: R 53 LYS cc_start: 0.6701 (ttmt) cc_final: 0.5564 (ttpp) REVERT: R 64 GLU cc_start: 0.6068 (mt-10) cc_final: 0.5858 (mt-10) REVERT: S 14 GLN cc_start: 0.6388 (mm-40) cc_final: 0.5395 (pt0) REVERT: S 27 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6524 (mm-30) REVERT: S 53 LYS cc_start: 0.6722 (ttmt) cc_final: 0.5597 (ttpp) REVERT: T 17 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6409 (tt0) REVERT: T 53 LYS cc_start: 0.6716 (ttmt) cc_final: 0.5696 (ttpp) REVERT: U 27 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6700 (mm-30) REVERT: U 53 LYS cc_start: 0.6698 (ttmt) cc_final: 0.5688 (ttpp) REVERT: U 140 GLU cc_start: 0.6441 (mm-30) cc_final: 0.5190 (mp0) REVERT: V 53 LYS cc_start: 0.6761 (ttmt) cc_final: 0.5638 (ttpp) REVERT: V 140 GLU cc_start: 0.6404 (mm-30) cc_final: 0.5200 (mp0) REVERT: W 53 LYS cc_start: 0.6677 (ttmt) cc_final: 0.5543 (ttpp) REVERT: W 71 LYS cc_start: 0.6027 (ttpp) cc_final: 0.5806 (ttpp) REVERT: W 140 GLU cc_start: 0.6400 (mm-30) cc_final: 0.5214 (mp0) REVERT: X 53 LYS cc_start: 0.6699 (ttmt) cc_final: 0.5679 (ttpp) REVERT: X 71 LYS cc_start: 0.6078 (ttpp) cc_final: 0.5832 (ttpp) REVERT: X 140 GLU cc_start: 0.6423 (mm-30) cc_final: 0.5232 (mp0) outliers start: 68 outliers final: 48 residues processed: 619 average time/residue: 2.9940 time to fit residues: 2179.0366 Evaluate side-chains 643 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 583 time to evaluate : 4.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain L residue 113 SER Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 27 GLU Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 94 GLU Chi-restraints excluded: chain Q residue 94 GLU Chi-restraints excluded: chain Q residue 113 SER Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 68 LYS Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 27 GLU Chi-restraints excluded: chain S residue 113 SER Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 17 GLU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain U residue 27 GLU Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 113 SER Chi-restraints excluded: chain X residue 165 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 chunk 267 optimal weight: 4.9990 chunk 194 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 309 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 34512 Z= 0.314 Angle : 0.568 6.198 46416 Z= 0.306 Chirality : 0.036 0.177 4848 Planarity : 0.004 0.035 6096 Dihedral : 5.034 58.547 4524 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.19 % Allowed : 18.26 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.57 (0.13), residues: 4080 helix: 2.98 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.18 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP C 93 HIS 0.004 0.001 HIS X 128 PHE 0.016 0.003 PHE R 41 TYR 0.016 0.002 TYR I 137 ARG 0.007 0.001 ARG X 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 667 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 587 time to evaluate : 4.237 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: symmetry clash REVERT: A 27 GLU cc_start: 0.6045 (mm-30) cc_final: 0.5380 (mm-30) REVERT: A 53 LYS cc_start: 0.6742 (ttmt) cc_final: 0.5589 (ttpp) REVERT: A 64 GLU cc_start: 0.6106 (mt-10) cc_final: 0.5872 (mt-10) REVERT: A 140 GLU cc_start: 0.6411 (mm-30) cc_final: 0.5215 (mp0) REVERT: B 15 ASP cc_start: 0.6888 (p0) cc_final: 0.6232 (m-30) REVERT: B 53 LYS cc_start: 0.6776 (ttmt) cc_final: 0.5640 (ttpp) REVERT: B 71 LYS cc_start: 0.6088 (ttpp) cc_final: 0.5868 (ttpp) REVERT: B 140 GLU cc_start: 0.6416 (mm-30) cc_final: 0.5237 (mp0) REVERT: C 53 LYS cc_start: 0.6766 (ttmt) cc_final: 0.5610 (ttpp) REVERT: C 63 ARG cc_start: 0.6506 (OUTLIER) cc_final: 0.6044 (tmm160) REVERT: C 143 LYS cc_start: 0.6076 (ttpp) cc_final: 0.5239 (mttm) REVERT: D 53 LYS cc_start: 0.6772 (ttmt) cc_final: 0.5615 (ttpp) REVERT: D 140 GLU cc_start: 0.6419 (mm-30) cc_final: 0.5209 (mp0) REVERT: E 27 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6101 (mt-10) REVERT: E 53 LYS cc_start: 0.6764 (ttmt) cc_final: 0.5725 (ttpp) REVERT: E 71 LYS cc_start: 0.6053 (ttpp) cc_final: 0.5810 (ttpp) REVERT: F 53 LYS cc_start: 0.6770 (ttmt) cc_final: 0.5612 (ttpp) REVERT: G 17 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6567 (tt0) REVERT: G 140 GLU cc_start: 0.6417 (mm-30) cc_final: 0.5168 (mp0) REVERT: H 64 GLU cc_start: 0.6101 (mt-10) cc_final: 0.5766 (mt-10) REVERT: I 17 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6558 (tt0) REVERT: I 53 LYS cc_start: 0.6740 (ttmt) cc_final: 0.5604 (ttpp) REVERT: I 140 GLU cc_start: 0.6420 (mm-30) cc_final: 0.5214 (mp0) REVERT: J 27 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6544 (mm-30) REVERT: J 53 LYS cc_start: 0.6739 (ttmt) cc_final: 0.5588 (ttpp) REVERT: K 53 LYS cc_start: 0.6759 (ttmt) cc_final: 0.5601 (ttpp) REVERT: K 64 GLU cc_start: 0.6141 (mt-10) cc_final: 0.5825 (mt-10) REVERT: K 71 LYS cc_start: 0.6042 (ttpp) cc_final: 0.5762 (ttpp) REVERT: L 53 LYS cc_start: 0.6766 (ttmt) cc_final: 0.5609 (ttpp) REVERT: L 67 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6906 (mt-10) REVERT: M 17 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6518 (tt0) REVERT: M 53 LYS cc_start: 0.6764 (ttmt) cc_final: 0.5615 (ttpp) REVERT: M 140 GLU cc_start: 0.6403 (mm-30) cc_final: 0.5208 (mp0) REVERT: N 53 LYS cc_start: 0.6727 (ttmt) cc_final: 0.5587 (ttpp) REVERT: N 71 LYS cc_start: 0.6175 (ttpp) cc_final: 0.5949 (ttpp) REVERT: O 27 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6491 (mm-30) REVERT: O 53 LYS cc_start: 0.6764 (ttmt) cc_final: 0.5607 (ttpp) REVERT: O 71 LYS cc_start: 0.6096 (ttpp) cc_final: 0.5843 (ttpp) REVERT: O 119 LYS cc_start: 0.6523 (tttt) cc_final: 0.5631 (ttpp) REVERT: P 27 GLU cc_start: 0.6113 (mm-30) cc_final: 0.5428 (mm-30) REVERT: P 53 LYS cc_start: 0.6746 (ttmt) cc_final: 0.5583 (ttpp) REVERT: P 140 GLU cc_start: 0.6387 (mm-30) cc_final: 0.5214 (mp0) REVERT: Q 27 GLU cc_start: 0.6136 (mm-30) cc_final: 0.5518 (mm-30) REVERT: Q 53 LYS cc_start: 0.6753 (ttmt) cc_final: 0.5609 (ttpp) REVERT: Q 140 GLU cc_start: 0.6399 (mm-30) cc_final: 0.5195 (mp0) REVERT: R 53 LYS cc_start: 0.6743 (ttmt) cc_final: 0.5590 (ttpp) REVERT: R 64 GLU cc_start: 0.6039 (mt-10) cc_final: 0.5796 (mt-10) REVERT: S 27 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6571 (mm-30) REVERT: S 53 LYS cc_start: 0.6728 (ttmt) cc_final: 0.5586 (ttpp) REVERT: T 53 LYS cc_start: 0.6760 (ttmt) cc_final: 0.5603 (ttpp) REVERT: U 27 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6183 (mt-10) REVERT: U 53 LYS cc_start: 0.6767 (ttmt) cc_final: 0.5619 (ttpp) REVERT: U 140 GLU cc_start: 0.6417 (mm-30) cc_final: 0.5214 (mp0) REVERT: V 53 LYS cc_start: 0.6772 (ttmt) cc_final: 0.5638 (ttpp) REVERT: V 140 GLU cc_start: 0.6402 (mm-30) cc_final: 0.5210 (mp0) REVERT: W 53 LYS cc_start: 0.6776 (ttmt) cc_final: 0.5624 (ttpp) REVERT: W 140 GLU cc_start: 0.6383 (mm-30) cc_final: 0.5197 (mp0) REVERT: X 53 LYS cc_start: 0.6737 (ttmt) cc_final: 0.5581 (ttpp) REVERT: X 140 GLU cc_start: 0.6408 (mm-30) cc_final: 0.5227 (mp0) outliers start: 80 outliers final: 59 residues processed: 631 average time/residue: 2.9978 time to fit residues: 2226.1220 Evaluate side-chains 647 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 578 time to evaluate : 4.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain L residue 113 SER Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 27 GLU Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 94 GLU Chi-restraints excluded: chain P residue 113 SER Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain P residue 167 GLU Chi-restraints excluded: chain Q residue 94 GLU Chi-restraints excluded: chain Q residue 113 SER Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 68 LYS Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 27 GLU Chi-restraints excluded: chain S residue 113 SER Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain U residue 27 GLU Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 113 SER Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 113 SER Chi-restraints excluded: chain X residue 165 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 2.9990 chunk 376 optimal weight: 1.9990 chunk 343 optimal weight: 2.9990 chunk 366 optimal weight: 0.6980 chunk 220 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 287 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 331 optimal weight: 2.9990 chunk 346 optimal weight: 4.9990 chunk 365 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 34512 Z= 0.218 Angle : 0.520 5.929 46416 Z= 0.279 Chirality : 0.033 0.159 4848 Planarity : 0.003 0.027 6096 Dihedral : 4.818 59.132 4524 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.59 % Allowed : 19.13 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.97 (0.13), residues: 4080 helix: 3.26 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.02 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP A 93 HIS 0.003 0.001 HIS T 128 PHE 0.014 0.002 PHE E 41 TYR 0.013 0.001 TYR I 137 ARG 0.006 0.000 ARG V 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 651 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 593 time to evaluate : 4.091 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: symmetry clash REVERT: A 27 GLU cc_start: 0.6010 (mm-30) cc_final: 0.5418 (mm-30) REVERT: A 53 LYS cc_start: 0.6700 (ttmt) cc_final: 0.5678 (ttpp) REVERT: A 64 GLU cc_start: 0.6069 (mt-10) cc_final: 0.5848 (mt-10) REVERT: A 119 LYS cc_start: 0.5674 (mmtm) cc_final: 0.5397 (ttmt) REVERT: A 140 GLU cc_start: 0.6415 (mm-30) cc_final: 0.5179 (mp0) REVERT: B 15 ASP cc_start: 0.6858 (p0) cc_final: 0.6278 (m-30) REVERT: B 53 LYS cc_start: 0.6691 (ttmt) cc_final: 0.5580 (ttpp) REVERT: B 71 LYS cc_start: 0.6042 (ttpp) cc_final: 0.5836 (ttpp) REVERT: B 140 GLU cc_start: 0.6428 (mm-30) cc_final: 0.5185 (mp0) REVERT: C 53 LYS cc_start: 0.6734 (ttmt) cc_final: 0.5613 (ttpp) REVERT: C 63 ARG cc_start: 0.6465 (OUTLIER) cc_final: 0.5595 (tmm160) REVERT: C 143 LYS cc_start: 0.6061 (ttpp) cc_final: 0.5234 (mttm) REVERT: D 53 LYS cc_start: 0.6658 (ttmt) cc_final: 0.5525 (ttpp) REVERT: D 140 GLU cc_start: 0.6445 (mm-30) cc_final: 0.5194 (mp0) REVERT: E 27 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6529 (mm-30) REVERT: E 53 LYS cc_start: 0.6713 (ttmt) cc_final: 0.5707 (ttpp) REVERT: F 53 LYS cc_start: 0.6734 (ttmt) cc_final: 0.5606 (ttpp) REVERT: G 17 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6464 (tt0) REVERT: G 140 GLU cc_start: 0.6418 (mm-30) cc_final: 0.5159 (mp0) REVERT: H 64 GLU cc_start: 0.6091 (mt-10) cc_final: 0.5772 (mt-10) REVERT: I 17 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6559 (tt0) REVERT: I 53 LYS cc_start: 0.6665 (ttmt) cc_final: 0.5540 (ttpp) REVERT: I 140 GLU cc_start: 0.6448 (mm-30) cc_final: 0.5227 (mp0) REVERT: J 27 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6462 (mm-30) REVERT: J 53 LYS cc_start: 0.6709 (ttmt) cc_final: 0.5586 (ttpp) REVERT: J 64 GLU cc_start: 0.6190 (mt-10) cc_final: 0.5866 (mt-10) REVERT: K 53 LYS cc_start: 0.6726 (ttmt) cc_final: 0.5600 (ttpp) REVERT: K 64 GLU cc_start: 0.6120 (mt-10) cc_final: 0.5871 (mt-10) REVERT: K 71 LYS cc_start: 0.5985 (ttpp) cc_final: 0.5735 (ttpp) REVERT: K 119 LYS cc_start: 0.6393 (ttpp) cc_final: 0.5905 (ttmt) REVERT: L 17 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.6321 (tt0) REVERT: L 53 LYS cc_start: 0.6649 (ttmt) cc_final: 0.5518 (ttpp) REVERT: L 67 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6830 (mt-10) REVERT: M 17 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6514 (tt0) REVERT: M 53 LYS cc_start: 0.6589 (ttmt) cc_final: 0.5461 (ttpp) REVERT: M 140 GLU cc_start: 0.6447 (mm-30) cc_final: 0.5187 (mp0) REVERT: N 53 LYS cc_start: 0.6705 (ttmt) cc_final: 0.5583 (ttpp) REVERT: N 71 LYS cc_start: 0.6043 (ttpp) cc_final: 0.5841 (ttpp) REVERT: O 27 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6387 (mm-30) REVERT: O 53 LYS cc_start: 0.6725 (ttmt) cc_final: 0.5704 (ttpp) REVERT: O 64 GLU cc_start: 0.6145 (mt-10) cc_final: 0.5844 (mt-10) REVERT: O 71 LYS cc_start: 0.6052 (ttpp) cc_final: 0.5812 (ttpp) REVERT: O 119 LYS cc_start: 0.6507 (tttt) cc_final: 0.5582 (ttpp) REVERT: P 27 GLU cc_start: 0.6053 (mm-30) cc_final: 0.5434 (mm-30) REVERT: P 53 LYS cc_start: 0.6633 (ttmt) cc_final: 0.5501 (ttpp) REVERT: P 71 LYS cc_start: 0.6003 (ttpp) cc_final: 0.5746 (ttpp) REVERT: P 140 GLU cc_start: 0.6388 (mm-30) cc_final: 0.5211 (mp0) REVERT: Q 27 GLU cc_start: 0.6038 (mm-30) cc_final: 0.5430 (mm-30) REVERT: Q 53 LYS cc_start: 0.6715 (ttmt) cc_final: 0.5591 (ttpp) REVERT: Q 140 GLU cc_start: 0.6457 (mm-30) cc_final: 0.5237 (mp0) REVERT: R 53 LYS cc_start: 0.6693 (ttmt) cc_final: 0.5553 (ttpp) REVERT: S 27 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6505 (mm-30) REVERT: S 53 LYS cc_start: 0.6713 (ttmt) cc_final: 0.5589 (ttpp) REVERT: T 17 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6387 (tt0) REVERT: T 53 LYS cc_start: 0.6725 (ttmt) cc_final: 0.5599 (ttpp) REVERT: T 143 LYS cc_start: 0.6074 (ttpp) cc_final: 0.5252 (mttm) REVERT: U 27 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6706 (mm-30) REVERT: U 53 LYS cc_start: 0.6734 (ttmt) cc_final: 0.5613 (ttpp) REVERT: U 140 GLU cc_start: 0.6442 (mm-30) cc_final: 0.5187 (mp0) REVERT: V 53 LYS cc_start: 0.6749 (ttmt) cc_final: 0.5625 (ttpp) REVERT: V 140 GLU cc_start: 0.6417 (mm-30) cc_final: 0.5210 (mp0) REVERT: W 53 LYS cc_start: 0.6679 (ttmt) cc_final: 0.5544 (ttpp) REVERT: W 140 GLU cc_start: 0.6399 (mm-30) cc_final: 0.5203 (mp0) REVERT: X 53 LYS cc_start: 0.6708 (ttmt) cc_final: 0.5576 (ttpp) REVERT: X 140 GLU cc_start: 0.6411 (mm-30) cc_final: 0.5234 (mp0) outliers start: 58 outliers final: 45 residues processed: 611 average time/residue: 2.9676 time to fit residues: 2133.1587 Evaluate side-chains 648 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 591 time to evaluate : 4.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain L residue 113 SER Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 27 GLU Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 94 GLU Chi-restraints excluded: chain P residue 113 SER Chi-restraints excluded: chain Q residue 94 GLU Chi-restraints excluded: chain Q residue 113 SER Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 68 LYS Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 27 GLU Chi-restraints excluded: chain S residue 113 SER Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 17 GLU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain U residue 27 GLU Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 113 SER Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 165 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 3.9990 chunk 387 optimal weight: 0.9980 chunk 236 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 269 optimal weight: 2.9990 chunk 406 optimal weight: 2.9990 chunk 374 optimal weight: 3.9990 chunk 323 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 250 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 10 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 34512 Z= 0.302 Angle : 0.567 6.406 46416 Z= 0.304 Chirality : 0.036 0.167 4848 Planarity : 0.004 0.033 6096 Dihedral : 4.970 57.874 4524 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.78 % Allowed : 19.02 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.64 (0.13), residues: 4080 helix: 3.03 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.14 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP C 93 HIS 0.004 0.001 HIS B 128 PHE 0.016 0.002 PHE N 41 TYR 0.015 0.002 TYR I 137 ARG 0.008 0.001 ARG X 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 645 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 580 time to evaluate : 4.095 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 27 GLU cc_start: 0.6046 (mm-30) cc_final: 0.5389 (mm-30) REVERT: A 53 LYS cc_start: 0.6728 (ttmt) cc_final: 0.5583 (ttpp) REVERT: A 64 GLU cc_start: 0.6098 (mt-10) cc_final: 0.5889 (mt-10) REVERT: A 119 LYS cc_start: 0.5669 (mmtm) cc_final: 0.5410 (ttmt) REVERT: A 140 GLU cc_start: 0.6423 (mm-30) cc_final: 0.5229 (mp0) REVERT: B 15 ASP cc_start: 0.6869 (p0) cc_final: 0.6238 (m-30) REVERT: B 53 LYS cc_start: 0.6775 (ttmt) cc_final: 0.5640 (ttpp) REVERT: B 71 LYS cc_start: 0.6077 (ttpp) cc_final: 0.5861 (ttpp) REVERT: B 140 GLU cc_start: 0.6415 (mm-30) cc_final: 0.5220 (mp0) REVERT: C 53 LYS cc_start: 0.6766 (ttmt) cc_final: 0.5624 (ttpp) REVERT: C 63 ARG cc_start: 0.6499 (OUTLIER) cc_final: 0.6005 (tmm160) REVERT: C 64 GLU cc_start: 0.6085 (mt-10) cc_final: 0.5787 (mt-10) REVERT: C 143 LYS cc_start: 0.6078 (ttpp) cc_final: 0.5236 (mttm) REVERT: D 53 LYS cc_start: 0.6774 (ttmt) cc_final: 0.5625 (ttpp) REVERT: D 140 GLU cc_start: 0.6425 (mm-30) cc_final: 0.5221 (mp0) REVERT: E 27 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6008 (mt-10) REVERT: E 53 LYS cc_start: 0.6754 (ttmt) cc_final: 0.5616 (ttpp) REVERT: F 53 LYS cc_start: 0.6772 (ttmt) cc_final: 0.5622 (ttpp) REVERT: G 140 GLU cc_start: 0.6406 (mm-30) cc_final: 0.5170 (mp0) REVERT: H 64 GLU cc_start: 0.6086 (mt-10) cc_final: 0.5760 (mt-10) REVERT: I 17 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6557 (tt0) REVERT: I 53 LYS cc_start: 0.6739 (ttmt) cc_final: 0.5604 (ttpp) REVERT: I 140 GLU cc_start: 0.6421 (mm-30) cc_final: 0.5213 (mp0) REVERT: J 27 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6543 (mm-30) REVERT: J 53 LYS cc_start: 0.6736 (ttmt) cc_final: 0.5587 (ttpp) REVERT: J 64 GLU cc_start: 0.6180 (mt-10) cc_final: 0.5929 (mt-10) REVERT: K 27 GLU cc_start: 0.6412 (mm-30) cc_final: 0.5725 (mm-30) REVERT: K 53 LYS cc_start: 0.6757 (ttmt) cc_final: 0.5613 (ttpp) REVERT: K 64 GLU cc_start: 0.6146 (mt-10) cc_final: 0.5892 (mt-10) REVERT: K 71 LYS cc_start: 0.6026 (ttpp) cc_final: 0.5754 (ttpp) REVERT: L 53 LYS cc_start: 0.6762 (ttmt) cc_final: 0.5609 (ttpp) REVERT: L 67 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6952 (mt-10) REVERT: M 17 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6509 (tt0) REVERT: M 53 LYS cc_start: 0.6762 (ttmt) cc_final: 0.5616 (ttpp) REVERT: M 140 GLU cc_start: 0.6406 (mm-30) cc_final: 0.5212 (mp0) REVERT: N 53 LYS cc_start: 0.6724 (ttmt) cc_final: 0.5585 (ttpp) REVERT: N 71 LYS cc_start: 0.6149 (ttpp) cc_final: 0.5927 (ttpp) REVERT: O 27 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6509 (mm-30) REVERT: O 53 LYS cc_start: 0.6762 (ttmt) cc_final: 0.5613 (ttpp) REVERT: O 64 GLU cc_start: 0.6138 (mt-10) cc_final: 0.5838 (mt-10) REVERT: O 71 LYS cc_start: 0.6097 (ttpp) cc_final: 0.5847 (ttpp) REVERT: O 119 LYS cc_start: 0.6511 (tttt) cc_final: 0.5622 (ttpp) REVERT: P 27 GLU cc_start: 0.6108 (mm-30) cc_final: 0.5432 (mm-30) REVERT: P 53 LYS cc_start: 0.6738 (ttmt) cc_final: 0.5595 (ttpp) REVERT: P 71 LYS cc_start: 0.6045 (ttpp) cc_final: 0.5775 (ttpp) REVERT: P 140 GLU cc_start: 0.6391 (mm-30) cc_final: 0.5212 (mp0) REVERT: Q 27 GLU cc_start: 0.6144 (mm-30) cc_final: 0.5533 (mm-30) REVERT: Q 53 LYS cc_start: 0.6740 (ttmt) cc_final: 0.5604 (ttpp) REVERT: Q 140 GLU cc_start: 0.6422 (mm-30) cc_final: 0.5212 (mp0) REVERT: R 53 LYS cc_start: 0.6737 (ttmt) cc_final: 0.5584 (ttpp) REVERT: S 27 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6580 (mm-30) REVERT: S 53 LYS cc_start: 0.6735 (ttmt) cc_final: 0.5608 (ttpp) REVERT: T 53 LYS cc_start: 0.6758 (ttmt) cc_final: 0.5603 (ttpp) REVERT: U 27 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6173 (mt-10) REVERT: U 53 LYS cc_start: 0.6753 (ttmt) cc_final: 0.5615 (ttpp) REVERT: U 140 GLU cc_start: 0.6419 (mm-30) cc_final: 0.5219 (mp0) REVERT: V 53 LYS cc_start: 0.6770 (ttmt) cc_final: 0.5639 (ttpp) REVERT: V 140 GLU cc_start: 0.6405 (mm-30) cc_final: 0.5220 (mp0) REVERT: W 53 LYS cc_start: 0.6777 (ttmt) cc_final: 0.5631 (ttpp) REVERT: W 140 GLU cc_start: 0.6400 (mm-30) cc_final: 0.5201 (mp0) REVERT: X 53 LYS cc_start: 0.6740 (ttmt) cc_final: 0.5591 (ttpp) REVERT: X 140 GLU cc_start: 0.6431 (mm-30) cc_final: 0.5242 (mp0) outliers start: 65 outliers final: 53 residues processed: 614 average time/residue: 2.9849 time to fit residues: 2156.1057 Evaluate side-chains 640 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 578 time to evaluate : 4.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain L residue 113 SER Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 27 GLU Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 94 GLU Chi-restraints excluded: chain P residue 113 SER Chi-restraints excluded: chain Q residue 94 GLU Chi-restraints excluded: chain Q residue 113 SER Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 68 LYS Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 27 GLU Chi-restraints excluded: chain S residue 113 SER Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain U residue 27 GLU Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 113 SER Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 165 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 3.9990 chunk 344 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 324 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 332 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.125094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.117989 restraints weight = 58572.198| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 0.36 r_work: 0.3175 rms_B_bonded: 0.54 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 1.08 restraints_weight: 0.2500 r_work: 0.2831 rms_B_bonded: 3.79 restraints_weight: 0.1250 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 34512 Z= 0.321 Angle : 0.575 6.504 46416 Z= 0.309 Chirality : 0.037 0.162 4848 Planarity : 0.004 0.032 6096 Dihedral : 4.994 57.043 4524 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.89 % Allowed : 18.97 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.53 (0.13), residues: 4080 helix: 2.96 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.21 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 93 HIS 0.004 0.001 HIS E 128 PHE 0.017 0.003 PHE E 41 TYR 0.016 0.002 TYR X 137 ARG 0.007 0.001 ARG X 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27978.78 seconds wall clock time: 478 minutes 53.25 seconds (28733.25 seconds total)