Starting phenix.real_space_refine on Mon Dec 30 23:02:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tue_41622/12_2024/8tue_41622.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tue_41622/12_2024/8tue_41622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tue_41622/12_2024/8tue_41622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tue_41622/12_2024/8tue_41622.map" model { file = "/net/cci-nas-00/data/ceres_data/8tue_41622/12_2024/8tue_41622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tue_41622/12_2024/8tue_41622.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.121 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 72 residue(s): 0.07s 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: 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: "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: 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: "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: 23.15, per 1000 atoms: 0.35 Number of scatterers: 66246 At special positions: 0 Unit cell: (132.24, 131.37, 131.37, 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: 13.17 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" ND1 HIS A 65 " pdb=" ZN B 201 " pdb="ZN ZN B 201 " - 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 202 " pdb="ZN ZN P 202 " - 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 202 " pdb="ZN ZN W 202 " - 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: 3.04 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: 3.979A pdb=" N GLU A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.813A 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: 3.913A pdb=" N GLU B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 3.695A 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: 3.978A pdb=" N GLU C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 3.791A 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: 3.933A pdb=" N GLU D 167 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 3.809A 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: 3.949A pdb=" N GLU E 167 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 3.728A 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: 3.935A pdb=" N GLU F 167 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 3.721A 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: 3.988A pdb=" N GLU G 167 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 3.805A 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: 3.983A pdb=" N GLU H 167 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 3.795A 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: 3.946A pdb=" N GLU I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 3.789A 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: 3.977A pdb=" N GLU J 167 " --> pdb=" O ALA J 163 " (cutoff:3.500A) removed outlier: 3.752A 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: 3.967A pdb=" N GLU K 167 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 3.778A 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: 3.970A pdb=" N GLU L 167 " --> pdb=" O ALA L 163 " (cutoff:3.500A) removed outlier: 3.781A 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: 4.032A pdb=" N GLU M 167 " --> pdb=" O ALA M 163 " (cutoff:3.500A) removed outlier: 3.810A 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: 3.954A pdb=" N GLU N 167 " --> pdb=" O ALA N 163 " (cutoff:3.500A) removed outlier: 3.760A 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: 3.949A pdb=" N GLU O 167 " --> pdb=" O ALA O 163 " (cutoff:3.500A) removed outlier: 3.720A 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: 3.951A pdb=" N GLU P 167 " --> pdb=" O ALA P 163 " (cutoff:3.500A) removed outlier: 3.791A 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: 3.975A pdb=" N GLU Q 167 " --> pdb=" O ALA Q 163 " (cutoff:3.500A) removed outlier: 3.749A 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: 3.934A pdb=" N GLU R 167 " --> pdb=" O ALA R 163 " (cutoff:3.500A) removed outlier: 3.777A 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: 3.986A pdb=" N GLU S 167 " --> pdb=" O ALA S 163 " (cutoff:3.500A) removed outlier: 3.790A 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: 3.914A pdb=" N GLU T 167 " --> pdb=" O ALA T 163 " (cutoff:3.500A) removed outlier: 3.765A 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: 3.953A pdb=" N GLU U 167 " --> pdb=" O ALA U 163 " (cutoff:3.500A) removed outlier: 3.774A 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: 3.982A pdb=" N GLU V 167 " --> pdb=" O ALA V 163 " (cutoff:3.500A) removed outlier: 3.804A 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: 3.851A pdb=" N GLU W 167 " --> pdb=" O ALA W 163 " (cutoff:3.500A) removed outlier: 3.726A 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: 4.003A pdb=" N GLU X 167 " --> pdb=" O ALA X 163 " (cutoff:3.500A) removed outlier: 3.774A 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: 21.81 Time building geometry restraints manager: 15.93 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: 97 1.23 - 1.42: 14951 1.42 - 1.62: 19224 1.62 - 1.81: 312 Bond restraints: 66912 Sorted by residual: bond pdb=" CG1 ILE Q 24 " pdb=" CD1 ILE Q 24 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.92e+00 bond pdb=" CG1 ILE I 24 " pdb=" CD1 ILE I 24 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.84e+00 bond pdb=" CG1 ILE E 24 " pdb=" CD1 ILE E 24 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.23e+00 bond pdb=" CG PRO F 161 " pdb=" CD PRO F 161 " ideal model delta sigma weight residual 1.512 1.483 0.029 2.70e-02 1.37e+03 1.13e+00 bond pdb=" CG PRO N 161 " pdb=" CD PRO N 161 " ideal model delta sigma weight residual 1.512 1.484 0.028 2.70e-02 1.37e+03 1.08e+00 ... (remaining 66907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 116385 1.29 - 2.58: 3639 2.58 - 3.86: 237 3.86 - 5.15: 38 5.15 - 6.44: 13 Bond angle restraints: 120312 Sorted by residual: angle pdb=" C TRP U 93 " pdb=" N GLU U 94 " pdb=" CA GLU U 94 " ideal model delta sigma weight residual 121.54 127.98 -6.44 1.91e+00 2.74e-01 1.14e+01 angle pdb=" C TRP J 93 " pdb=" N GLU J 94 " pdb=" CA GLU J 94 " ideal model delta sigma weight residual 121.54 127.66 -6.12 1.91e+00 2.74e-01 1.03e+01 angle pdb=" C TRP S 93 " pdb=" N GLU S 94 " pdb=" CA GLU S 94 " ideal model delta sigma weight residual 121.54 127.60 -6.06 1.91e+00 2.74e-01 1.01e+01 angle pdb=" C TRP Q 93 " pdb=" N GLU Q 94 " pdb=" CA GLU Q 94 " ideal model delta sigma weight residual 121.54 127.37 -5.83 1.91e+00 2.74e-01 9.31e+00 angle pdb=" C TRP E 93 " pdb=" N GLU E 94 " pdb=" CA GLU E 94 " ideal model delta sigma weight residual 121.54 127.33 -5.79 1.91e+00 2.74e-01 9.18e+00 ... (remaining 120307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 27967 18.03 - 36.06: 2403 36.06 - 54.08: 826 54.08 - 72.11: 239 72.11 - 90.14: 125 Dihedral angle restraints: 31560 sinusoidal: 16920 harmonic: 14640 Sorted by residual: dihedral pdb=" CA TRP S 93 " pdb=" C TRP S 93 " pdb=" N GLU S 94 " pdb=" CA GLU S 94 " ideal model delta harmonic sigma weight residual 180.00 157.78 22.22 0 5.00e+00 4.00e-02 1.97e+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 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA TRP J 93 " pdb=" C TRP J 93 " pdb=" N GLU J 94 " pdb=" CA GLU J 94 " ideal model delta harmonic sigma weight residual 180.00 159.19 20.81 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 31557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3630 0.029 - 0.059: 830 0.059 - 0.088: 245 0.088 - 0.117: 134 0.117 - 0.147: 9 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 2.36 0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA ILE I 24 " pdb=" N ILE I 24 " pdb=" C ILE I 24 " pdb=" CB ILE I 24 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE Q 24 " pdb=" N ILE Q 24 " pdb=" C ILE Q 24 " pdb=" CB ILE Q 24 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 4845 not shown) Planarity restraints: 10128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP J 93 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C TRP J 93 " 0.028 2.00e-02 2.50e+03 pdb=" O TRP J 93 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU J 94 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP S 93 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" C TRP S 93 " -0.027 2.00e-02 2.50e+03 pdb=" O TRP S 93 " 0.010 2.00e-02 2.50e+03 pdb=" N GLU S 94 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP D 93 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C TRP D 93 " 0.025 2.00e-02 2.50e+03 pdb=" O TRP D 93 " -0.009 2.00e-02 2.50e+03 pdb=" N GLU D 94 " -0.008 2.00e-02 2.50e+03 ... (remaining 10125 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 1832 2.12 - 2.74: 121546 2.74 - 3.36: 226441 3.36 - 3.98: 287923 3.98 - 4.60: 439034 Nonbonded interactions: 1076776 Sorted by model distance: nonbonded pdb=" OE2 GLU W 17 " pdb=" H ARG W 79 " model vdw 1.496 2.450 nonbonded pdb=" OE2 GLU A 17 " pdb=" H ARG A 79 " model vdw 1.500 2.450 nonbonded pdb=" OE2 GLU U 17 " pdb=" H ARG U 79 " model vdw 1.502 2.450 nonbonded pdb=" OE2 GLU V 17 " pdb=" H ARG V 79 " model vdw 1.504 2.450 nonbonded pdb=" OE2 GLU Q 17 " pdb=" H ARG Q 79 " model vdw 1.512 2.450 ... (remaining 1076771 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.850 Extract box with map and model: 1.810 Check model and map are aligned: 0.370 Set scattering table: 0.470 Process input model: 125.780 Find NCS groups from input model: 2.430 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 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 : 0.003 0.054 34512 Z= 0.174 Angle : 0.504 6.440 46416 Z= 0.274 Chirality : 0.032 0.147 4848 Planarity : 0.003 0.023 6096 Dihedral : 18.504 90.138 13080 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.69 % Allowed : 14.78 % Favored : 84.54 % 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: 4.33 (0.13), residues: 4080 helix: 3.43 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : 0.54 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP X 93 HIS 0.003 0.001 HIS C 128 PHE 0.016 0.002 PHE N 41 TYR 0.009 0.001 TYR I 137 ARG 0.004 0.000 ARG X 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 637 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 612 time to evaluate : 4.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 14 GLN cc_start: 0.7437 (tp40) cc_final: 0.7211 (mm110) REVERT: F 89 ASP cc_start: 0.6837 (p0) cc_final: 0.6586 (p0) REVERT: G 89 ASP cc_start: 0.6588 (p0) cc_final: 0.6282 (p0) REVERT: H 14 GLN cc_start: 0.7486 (tp40) cc_final: 0.7252 (mm110) REVERT: I 14 GLN cc_start: 0.7496 (tp40) cc_final: 0.7248 (mm110) REVERT: K 89 ASP cc_start: 0.6690 (p0) cc_final: 0.6366 (p0) REVERT: L 89 ASP cc_start: 0.6824 (p0) cc_final: 0.6574 (p0) REVERT: N 14 GLN cc_start: 0.7335 (tp40) cc_final: 0.7125 (mm110) REVERT: R 89 ASP cc_start: 0.6862 (p0) cc_final: 0.6344 (p0) REVERT: X 14 GLN cc_start: 0.7469 (tp40) cc_final: 0.7241 (mm-40) REVERT: X 63 ARG cc_start: 0.7600 (ttp-170) cc_final: 0.6778 (ttp80) outliers start: 25 outliers final: 20 residues processed: 637 average time/residue: 3.1856 time to fit residues: 2367.0699 Evaluate side-chains 604 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 584 time to evaluate : 4.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain J residue 167 GLU Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain L residue 167 GLU Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain O residue 167 GLU Chi-restraints excluded: chain P residue 167 GLU Chi-restraints excluded: chain Q residue 167 GLU 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 167 GLU Chi-restraints excluded: chain V 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: 6.9990 chunk 309 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 319 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 238 optimal weight: 4.9990 chunk 370 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 7 GLN D 14 GLN J 14 GLN K 14 GLN L 7 GLN L 14 GLN O 7 GLN R 14 GLN S 14 GLN V 7 GLN V 75 GLN V 111 ASN X 7 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 34512 Z= 0.288 Angle : 0.575 6.891 46416 Z= 0.312 Chirality : 0.036 0.172 4848 Planarity : 0.004 0.031 6096 Dihedral : 6.690 55.603 4566 Min Nonbonded Distance : 1.549 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.12 % Allowed : 14.99 % Favored : 83.88 % 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: 4.10 (0.13), residues: 4080 helix: 3.28 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.47 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP O 93 HIS 0.005 0.001 HIS L 128 PHE 0.022 0.003 PHE A 41 TYR 0.017 0.002 TYR E 137 ARG 0.004 0.000 ARG X 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 623 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 582 time to evaluate : 4.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: B 63 ARG cc_start: 0.7682 (tpp80) cc_final: 0.7331 (tpp80) REVERT: B 167 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7954 (tt0) REVERT: C 167 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7979 (tt0) REVERT: E 53 LYS cc_start: 0.8037 (ttpt) cc_final: 0.7443 (ttpp) REVERT: E 63 ARG cc_start: 0.7660 (tpp80) cc_final: 0.7358 (tpp80) REVERT: G 167 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7897 (tt0) REVERT: H 14 GLN cc_start: 0.7530 (tp40) cc_final: 0.7327 (mm-40) REVERT: H 53 LYS cc_start: 0.8034 (ttpt) cc_final: 0.7432 (ttpp) REVERT: H 167 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: J 167 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7959 (tt0) REVERT: K 167 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: L 167 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7952 (tt0) REVERT: N 14 GLN cc_start: 0.7481 (tp40) cc_final: 0.7249 (mm-40) REVERT: N 116 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7442 (mm-30) REVERT: O 14 GLN cc_start: 0.7533 (tp-100) cc_final: 0.7333 (mm-40) REVERT: O 167 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7953 (tt0) REVERT: P 167 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7973 (tt0) REVERT: Q 167 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: R 167 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7922 (tt0) REVERT: S 116 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: S 167 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: T 167 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7935 (tt0) REVERT: V 167 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: X 14 GLN cc_start: 0.7549 (tp40) cc_final: 0.7327 (mm110) outliers start: 41 outliers final: 7 residues processed: 610 average time/residue: 3.1864 time to fit residues: 2267.9790 Evaluate side-chains 584 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 560 time to evaluate : 4.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 167 GLU Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain L residue 167 GLU Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain N residue 116 GLU Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain O residue 167 GLU Chi-restraints excluded: chain P residue 167 GLU Chi-restraints excluded: chain Q residue 167 GLU Chi-restraints excluded: chain R residue 167 GLU Chi-restraints excluded: chain S residue 116 GLU Chi-restraints excluded: chain S residue 167 GLU Chi-restraints excluded: chain T residue 167 GLU Chi-restraints excluded: chain V residue 167 GLU Chi-restraints excluded: chain W residue 167 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 308 optimal weight: 4.9990 chunk 252 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 371 optimal weight: 7.9990 chunk 400 optimal weight: 6.9990 chunk 330 optimal weight: 4.9990 chunk 368 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 297 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 14 GLN K 14 GLN L 14 GLN O 10 GLN ** O 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 34512 Z= 0.384 Angle : 0.634 6.964 46416 Z= 0.346 Chirality : 0.040 0.172 4848 Planarity : 0.005 0.042 6096 Dihedral : 6.000 46.391 4559 Min Nonbonded Distance : 1.466 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.07 % Allowed : 14.72 % Favored : 84.21 % 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: 2.99 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.16 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.005 TRP E 93 HIS 0.006 0.002 HIS I 128 PHE 0.027 0.003 PHE A 41 TYR 0.019 0.002 TYR E 137 ARG 0.005 0.001 ARG X 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 613 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 574 time to evaluate : 4.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 ARG cc_start: 0.7580 (tpp80) cc_final: 0.7296 (tpp80) REVERT: E 53 LYS cc_start: 0.8067 (ttpt) cc_final: 0.7453 (ttpp) REVERT: G 63 ARG cc_start: 0.7731 (tpp80) cc_final: 0.7376 (tpp80) REVERT: G 116 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7425 (mt-10) REVERT: H 53 LYS cc_start: 0.8049 (ttpt) cc_final: 0.7428 (ttpp) REVERT: I 116 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7566 (mt-10) REVERT: L 94 GLU cc_start: 0.7084 (pt0) cc_final: 0.6703 (pt0) REVERT: N 116 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7497 (mt-10) REVERT: P 63 ARG cc_start: 0.7602 (tpp80) cc_final: 0.7327 (tpp80) REVERT: S 63 ARG cc_start: 0.7609 (tpp80) cc_final: 0.7246 (tpp80) REVERT: S 116 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7493 (mt-10) REVERT: U 63 ARG cc_start: 0.7599 (tpp80) cc_final: 0.7290 (tpp80) REVERT: X 63 ARG cc_start: 0.7578 (ttp-170) cc_final: 0.6760 (ttp80) outliers start: 39 outliers final: 7 residues processed: 587 average time/residue: 3.3099 time to fit residues: 2252.4062 Evaluate side-chains 574 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 563 time to evaluate : 4.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain I residue 116 GLU Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain N residue 116 GLU Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain S residue 116 GLU Chi-restraints excluded: chain W residue 167 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 5.9990 chunk 279 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 249 optimal weight: 5.9990 chunk 372 optimal weight: 1.9990 chunk 394 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 353 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 111 ASN I 75 GLN J 10 GLN J 14 GLN K 14 GLN L 14 GLN O 111 ASN V 111 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 34512 Z= 0.277 Angle : 0.562 6.531 46416 Z= 0.306 Chirality : 0.036 0.145 4848 Planarity : 0.004 0.047 6096 Dihedral : 4.633 46.848 4514 Min Nonbonded Distance : 1.614 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.71 % Allowed : 15.60 % Favored : 83.69 % 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: 3.88 (0.13), residues: 4080 helix: 3.16 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.20 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP S 93 HIS 0.005 0.001 HIS L 128 PHE 0.022 0.003 PHE N 41 TYR 0.016 0.001 TYR E 137 ARG 0.002 0.000 ARG X 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 593 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 567 time to evaluate : 4.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 ARG cc_start: 0.7605 (tpp80) cc_final: 0.7326 (tpp80) REVERT: G 63 ARG cc_start: 0.7707 (tpp80) cc_final: 0.7449 (tpp80) REVERT: H 53 LYS cc_start: 0.8055 (ttpt) cc_final: 0.7436 (ttpp) REVERT: L 94 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6391 (mt-10) REVERT: P 63 ARG cc_start: 0.7589 (tpp80) cc_final: 0.7315 (tpp80) REVERT: Q 90 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7343 (pmt170) REVERT: S 63 ARG cc_start: 0.7566 (tpp80) cc_final: 0.7224 (tpp80) REVERT: S 116 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7366 (mp0) outliers start: 26 outliers final: 16 residues processed: 586 average time/residue: 3.3214 time to fit residues: 2269.0959 Evaluate side-chains 565 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 546 time to evaluate : 4.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain L residue 94 GLU Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 90 ARG Chi-restraints excluded: chain N residue 90 ARG Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain O residue 90 ARG Chi-restraints excluded: chain P residue 90 ARG Chi-restraints excluded: chain Q residue 90 ARG Chi-restraints excluded: chain S residue 90 ARG Chi-restraints excluded: chain S residue 116 GLU Chi-restraints excluded: chain U residue 167 GLU Chi-restraints excluded: chain W residue 167 GLU Chi-restraints excluded: chain X residue 90 ARG 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: 4.9990 chunk 5 optimal weight: 2.9990 chunk 293 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 336 optimal weight: 3.9990 chunk 272 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 chunk 353 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 14 GLN H 14 GLN J 14 GLN K 14 GLN L 14 GLN O 14 GLN P 14 GLN R 14 GLN S 111 ASN V 111 ASN X 14 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 34512 Z= 0.371 Angle : 0.623 6.953 46416 Z= 0.340 Chirality : 0.039 0.168 4848 Planarity : 0.005 0.043 6096 Dihedral : 4.769 47.601 4514 Min Nonbonded Distance : 1.472 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.77 % Allowed : 16.09 % Favored : 83.14 % 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: 3.58 (0.12), residues: 4080 helix: 2.97 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.02 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP O 93 HIS 0.006 0.002 HIS O 128 PHE 0.026 0.003 PHE N 41 TYR 0.019 0.002 TYR E 137 ARG 0.005 0.001 ARG X 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 581 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 553 time to evaluate : 4.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 ARG cc_start: 0.7641 (tpp80) cc_final: 0.7406 (tpp80) REVERT: H 53 LYS cc_start: 0.8064 (ttpt) cc_final: 0.7445 (ttpp) REVERT: L 94 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6479 (mt-10) REVERT: O 63 ARG cc_start: 0.7639 (tpp80) cc_final: 0.7343 (tpp80) REVERT: P 63 ARG cc_start: 0.7578 (tpp80) cc_final: 0.7291 (tpp80) REVERT: S 63 ARG cc_start: 0.7584 (tpp80) cc_final: 0.7272 (tpp80) REVERT: S 116 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7495 (mt-10) outliers start: 28 outliers final: 17 residues processed: 574 average time/residue: 3.3327 time to fit residues: 2221.9428 Evaluate side-chains 562 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 543 time to evaluate : 4.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain L residue 94 GLU Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 90 ARG Chi-restraints excluded: chain N residue 90 ARG Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain O residue 90 ARG Chi-restraints excluded: chain P residue 90 ARG Chi-restraints excluded: chain Q residue 90 ARG Chi-restraints excluded: chain S residue 90 ARG Chi-restraints excluded: chain S residue 116 GLU Chi-restraints excluded: chain U residue 167 GLU Chi-restraints excluded: chain W residue 167 GLU Chi-restraints excluded: chain X residue 90 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 3.9990 chunk 355 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 394 optimal weight: 3.9990 chunk 327 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 14 GLN H 14 GLN I 75 GLN J 14 GLN K 14 GLN L 14 GLN O 14 GLN O 111 ASN P 14 GLN Q 75 GLN R 14 GLN S 10 GLN X 14 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 34512 Z= 0.311 Angle : 0.584 6.539 46416 Z= 0.319 Chirality : 0.037 0.149 4848 Planarity : 0.004 0.045 6096 Dihedral : 4.707 47.982 4514 Min Nonbonded Distance : 1.597 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.63 % Allowed : 16.50 % Favored : 82.87 % 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: 3.68 (0.12), residues: 4080 helix: 3.05 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.03 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP O 93 HIS 0.005 0.001 HIS O 128 PHE 0.023 0.003 PHE N 41 TYR 0.017 0.002 TYR E 137 ARG 0.007 0.001 ARG X 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 570 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 547 time to evaluate : 4.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 ARG cc_start: 0.7627 (tpp80) cc_final: 0.7379 (tpp80) REVERT: H 53 LYS cc_start: 0.8059 (ttpt) cc_final: 0.7559 (ttpp) REVERT: K 63 ARG cc_start: 0.7676 (tpp80) cc_final: 0.7341 (tpp80) REVERT: L 94 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6817 (pt0) REVERT: O 63 ARG cc_start: 0.7565 (tpp80) cc_final: 0.7225 (tpp80) REVERT: P 63 ARG cc_start: 0.7611 (tpp80) cc_final: 0.7332 (tpp80) REVERT: S 63 ARG cc_start: 0.7611 (tpp80) cc_final: 0.7335 (tpp80) REVERT: S 116 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7506 (mt-10) REVERT: U 63 ARG cc_start: 0.7668 (tpp80) cc_final: 0.7335 (tpp80) REVERT: X 157 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8095 (mptm) outliers start: 23 outliers final: 17 residues processed: 565 average time/residue: 3.3038 time to fit residues: 2167.6870 Evaluate side-chains 563 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 543 time to evaluate : 4.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain L residue 94 GLU Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 90 ARG Chi-restraints excluded: chain N residue 90 ARG Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain O residue 90 ARG Chi-restraints excluded: chain P residue 90 ARG Chi-restraints excluded: chain Q residue 90 ARG Chi-restraints excluded: chain S residue 90 ARG Chi-restraints excluded: chain S residue 116 GLU Chi-restraints excluded: chain U residue 167 GLU Chi-restraints excluded: chain W residue 167 GLU Chi-restraints excluded: chain X residue 90 ARG Chi-restraints excluded: chain X residue 157 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 224 optimal weight: 4.9990 chunk 288 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 332 optimal weight: 5.9990 chunk 220 optimal weight: 3.9990 chunk 393 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 GLN F 14 GLN H 14 GLN J 14 GLN K 14 GLN L 14 GLN O 14 GLN P 14 GLN Q 14 GLN R 14 GLN U 14 GLN X 14 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 34512 Z= 0.305 Angle : 0.584 6.906 46416 Z= 0.318 Chirality : 0.037 0.144 4848 Planarity : 0.004 0.045 6096 Dihedral : 4.695 48.298 4514 Min Nonbonded Distance : 1.571 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.63 % Allowed : 16.47 % Favored : 82.89 % 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: 3.73 (0.12), residues: 4080 helix: 3.08 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.04 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP E 93 HIS 0.005 0.001 HIS K 128 PHE 0.023 0.003 PHE N 41 TYR 0.017 0.002 TYR E 137 ARG 0.005 0.001 ARG X 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 568 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 545 time to evaluate : 4.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7709 (tpp80) cc_final: 0.7385 (tpp80) REVERT: B 63 ARG cc_start: 0.7582 (tpp80) cc_final: 0.7335 (tpp80) REVERT: H 53 LYS cc_start: 0.8058 (ttpt) cc_final: 0.7558 (ttpp) REVERT: H 63 ARG cc_start: 0.7638 (tpp80) cc_final: 0.7319 (tpp80) REVERT: K 63 ARG cc_start: 0.7584 (tpp80) cc_final: 0.7261 (tpp80) REVERT: L 94 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6811 (pt0) REVERT: O 63 ARG cc_start: 0.7555 (tpp80) cc_final: 0.7242 (tpp80) REVERT: P 63 ARG cc_start: 0.7612 (tpp80) cc_final: 0.7347 (tpp80) REVERT: S 63 ARG cc_start: 0.7645 (tpp80) cc_final: 0.7392 (tpp80) REVERT: S 116 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7504 (mt-10) REVERT: X 157 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8100 (mptm) outliers start: 23 outliers final: 16 residues processed: 565 average time/residue: 3.2672 time to fit residues: 2147.8783 Evaluate side-chains 556 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 537 time to evaluate : 4.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain L residue 94 GLU Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 90 ARG Chi-restraints excluded: chain N residue 90 ARG Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain O residue 90 ARG Chi-restraints excluded: chain P residue 90 ARG Chi-restraints excluded: chain Q residue 90 ARG Chi-restraints excluded: chain S residue 90 ARG Chi-restraints excluded: chain S residue 116 GLU Chi-restraints excluded: chain U residue 167 GLU Chi-restraints excluded: chain W residue 167 GLU Chi-restraints excluded: chain X residue 90 ARG Chi-restraints excluded: chain X residue 157 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 234 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 chunk 267 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 309 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 GLN E 10 GLN E 14 GLN F 14 GLN H 14 GLN J 14 GLN K 14 GLN L 14 GLN O 14 GLN Q 14 GLN Q 75 GLN R 14 GLN U 14 GLN X 14 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 34512 Z= 0.304 Angle : 0.583 6.708 46416 Z= 0.318 Chirality : 0.037 0.144 4848 Planarity : 0.004 0.046 6096 Dihedral : 4.693 48.524 4514 Min Nonbonded Distance : 1.580 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.66 % Allowed : 16.50 % Favored : 82.84 % 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: 3.73 (0.12), residues: 4080 helix: 3.09 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.03 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP O 93 HIS 0.005 0.001 HIS O 128 PHE 0.023 0.003 PHE R 41 TYR 0.017 0.002 TYR E 137 ARG 0.004 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 566 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 542 time to evaluate : 4.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 ARG cc_start: 0.7579 (tpp80) cc_final: 0.7342 (tpp80) REVERT: D 63 ARG cc_start: 0.7587 (tpp80) cc_final: 0.7298 (tpp80) REVERT: H 53 LYS cc_start: 0.8060 (ttpt) cc_final: 0.7563 (ttpp) REVERT: I 63 ARG cc_start: 0.7635 (tpp80) cc_final: 0.7306 (tpp80) REVERT: K 89 ASP cc_start: 0.6782 (p0) cc_final: 0.6354 (p0) REVERT: L 94 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6815 (pt0) REVERT: N 63 ARG cc_start: 0.7626 (tpp80) cc_final: 0.7305 (tpp80) REVERT: O 63 ARG cc_start: 0.7595 (tpp80) cc_final: 0.7302 (tpp80) REVERT: P 63 ARG cc_start: 0.7636 (tpp80) cc_final: 0.7375 (tpp80) REVERT: Q 63 ARG cc_start: 0.7586 (tpp80) cc_final: 0.7303 (tpp80) REVERT: R 63 ARG cc_start: 0.7631 (tpp80) cc_final: 0.7302 (tpp80) REVERT: S 63 ARG cc_start: 0.7636 (tpp80) cc_final: 0.7383 (tpp80) REVERT: S 116 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7507 (mt-10) REVERT: W 63 ARG cc_start: 0.7581 (tpp80) cc_final: 0.7270 (tpp80) REVERT: X 157 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8097 (mptm) outliers start: 24 outliers final: 16 residues processed: 562 average time/residue: 3.2543 time to fit residues: 2127.4071 Evaluate side-chains 557 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 538 time to evaluate : 4.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain L residue 94 GLU Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 90 ARG Chi-restraints excluded: chain N residue 90 ARG Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain O residue 90 ARG Chi-restraints excluded: chain P residue 90 ARG Chi-restraints excluded: chain Q residue 90 ARG Chi-restraints excluded: chain S residue 90 ARG Chi-restraints excluded: chain S residue 116 GLU Chi-restraints excluded: chain U residue 167 GLU Chi-restraints excluded: chain W residue 167 GLU Chi-restraints excluded: chain X residue 90 ARG Chi-restraints excluded: chain X residue 157 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 4.9990 chunk 376 optimal weight: 3.9990 chunk 343 optimal weight: 3.9990 chunk 366 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 287 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 331 optimal weight: 0.9980 chunk 346 optimal weight: 6.9990 chunk 365 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 GLN E 14 GLN F 14 GLN H 14 GLN J 14 GLN K 14 GLN L 14 GLN M 14 GLN O 14 GLN Q 14 GLN Q 98 ASN R 14 GLN U 14 GLN V 14 GLN X 14 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 34512 Z= 0.244 Angle : 0.549 6.644 46416 Z= 0.298 Chirality : 0.035 0.132 4848 Planarity : 0.004 0.044 6096 Dihedral : 4.595 48.860 4514 Min Nonbonded Distance : 1.639 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.60 % Allowed : 16.56 % Favored : 82.84 % 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: 4.02 (0.13), residues: 4080 helix: 3.29 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.14 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 93 HIS 0.004 0.001 HIS O 128 PHE 0.019 0.002 PHE N 41 TYR 0.015 0.001 TYR I 137 ARG 0.004 0.000 ARG K 90 *********************** 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 573 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 551 time to evaluate : 4.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7727 (tpp80) cc_final: 0.7402 (tpp80) REVERT: B 63 ARG cc_start: 0.7604 (tpp80) cc_final: 0.7340 (tpp80) REVERT: D 63 ARG cc_start: 0.7583 (tpp80) cc_final: 0.7236 (tpp80) REVERT: E 63 ARG cc_start: 0.7674 (tpp80) cc_final: 0.7391 (tpp80) REVERT: F 63 ARG cc_start: 0.7680 (tpp80) cc_final: 0.7372 (tpp80) REVERT: F 89 ASP cc_start: 0.6947 (p0) cc_final: 0.6611 (p0) REVERT: G 89 ASP cc_start: 0.6784 (p0) cc_final: 0.6298 (p0) REVERT: H 63 ARG cc_start: 0.7667 (tpp80) cc_final: 0.7390 (tpp80) REVERT: I 63 ARG cc_start: 0.7602 (tpp80) cc_final: 0.7240 (tpp80) REVERT: J 63 ARG cc_start: 0.7621 (tpp80) cc_final: 0.7305 (tpp80) REVERT: K 63 ARG cc_start: 0.7687 (tpp80) cc_final: 0.7325 (tpp80) REVERT: L 89 ASP cc_start: 0.6956 (p0) cc_final: 0.6638 (p0) REVERT: L 94 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6788 (pt0) REVERT: N 63 ARG cc_start: 0.7643 (tpp80) cc_final: 0.7369 (tpp80) REVERT: O 63 ARG cc_start: 0.7598 (tpp80) cc_final: 0.7291 (tpp80) REVERT: P 63 ARG cc_start: 0.7570 (tpp80) cc_final: 0.7305 (tpp80) REVERT: Q 63 ARG cc_start: 0.7578 (tpp80) cc_final: 0.7289 (tpp80) REVERT: R 63 ARG cc_start: 0.7649 (tpp80) cc_final: 0.7314 (tpp80) REVERT: S 63 ARG cc_start: 0.7597 (tpp80) cc_final: 0.7325 (tpp80) REVERT: S 116 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7435 (mt-10) REVERT: T 14 GLN cc_start: 0.7446 (tp40) cc_final: 0.7239 (mm-40) REVERT: T 63 ARG cc_start: 0.7688 (tpp80) cc_final: 0.7377 (tpp80) REVERT: U 63 ARG cc_start: 0.7671 (tpp80) cc_final: 0.7364 (tpp80) REVERT: W 63 ARG cc_start: 0.7555 (tpp80) cc_final: 0.7278 (tpp80) REVERT: X 157 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8072 (mptm) outliers start: 22 outliers final: 16 residues processed: 569 average time/residue: 3.2166 time to fit residues: 2132.0749 Evaluate side-chains 555 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 536 time to evaluate : 4.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain L residue 94 GLU Chi-restraints excluded: chain M residue 90 ARG Chi-restraints excluded: chain N residue 90 ARG Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain O residue 90 ARG Chi-restraints excluded: chain P residue 90 ARG Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain S residue 90 ARG Chi-restraints excluded: chain S residue 116 GLU Chi-restraints excluded: chain U residue 167 GLU Chi-restraints excluded: chain W residue 167 GLU Chi-restraints excluded: chain X residue 90 ARG Chi-restraints excluded: chain X residue 157 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 5.9990 chunk 387 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 269 optimal weight: 6.9990 chunk 406 optimal weight: 4.9990 chunk 374 optimal weight: 5.9990 chunk 323 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 250 optimal weight: 0.7980 chunk 198 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN C 14 GLN D 14 GLN E 14 GLN F 14 GLN H 14 GLN J 14 GLN K 14 GLN L 14 GLN M 14 GLN N 14 GLN O 14 GLN O 111 ASN Q 14 GLN Q 75 GLN R 14 GLN U 14 GLN V 14 GLN W 14 GLN X 14 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 34512 Z= 0.279 Angle : 0.571 6.847 46416 Z= 0.310 Chirality : 0.036 0.141 4848 Planarity : 0.004 0.047 6096 Dihedral : 4.621 49.043 4513 Min Nonbonded Distance : 1.587 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.58 % Allowed : 16.56 % Favored : 82.87 % 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 (0.12), residues: 4080 helix: 3.21 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.10 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP B 93 HIS 0.005 0.001 HIS O 128 PHE 0.022 0.003 PHE R 41 TYR 0.017 0.002 TYR E 137 ARG 0.005 0.000 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 563 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 542 time to evaluate : 4.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7634 (tpp80) cc_final: 0.7352 (tpp80) REVERT: B 63 ARG cc_start: 0.7606 (tpp80) cc_final: 0.7355 (tpp80) REVERT: D 63 ARG cc_start: 0.7565 (tpp80) cc_final: 0.7253 (tpp80) REVERT: E 63 ARG cc_start: 0.7643 (tpp80) cc_final: 0.7359 (tpp80) REVERT: F 63 ARG cc_start: 0.7665 (tpp80) cc_final: 0.7355 (tpp80) REVERT: H 63 ARG cc_start: 0.7636 (tpp80) cc_final: 0.7356 (tpp80) REVERT: I 63 ARG cc_start: 0.7582 (tpp80) cc_final: 0.7224 (tpp80) REVERT: J 63 ARG cc_start: 0.7568 (tpp80) cc_final: 0.7296 (tpp80) REVERT: K 63 ARG cc_start: 0.7717 (tpp80) cc_final: 0.7427 (tpp80) REVERT: L 94 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6797 (pt0) REVERT: N 63 ARG cc_start: 0.7607 (tpp80) cc_final: 0.7276 (tpp80) REVERT: O 63 ARG cc_start: 0.7599 (tpp80) cc_final: 0.7312 (tpp80) REVERT: P 63 ARG cc_start: 0.7581 (tpp80) cc_final: 0.7315 (tpp80) REVERT: Q 63 ARG cc_start: 0.7572 (tpp80) cc_final: 0.7225 (tpp80) REVERT: R 63 ARG cc_start: 0.7607 (tpp80) cc_final: 0.7269 (tpp80) REVERT: S 63 ARG cc_start: 0.7606 (tpp80) cc_final: 0.7336 (tpp80) REVERT: S 116 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7431 (mt-10) REVERT: T 14 GLN cc_start: 0.7482 (tp40) cc_final: 0.7266 (mm-40) REVERT: T 63 ARG cc_start: 0.7676 (tpp80) cc_final: 0.7340 (tpp80) REVERT: U 63 ARG cc_start: 0.7616 (tpp80) cc_final: 0.7334 (tpp80) REVERT: W 63 ARG cc_start: 0.7552 (tpp80) cc_final: 0.7244 (tpp80) REVERT: X 157 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8048 (mptm) outliers start: 21 outliers final: 16 residues processed: 558 average time/residue: 3.2392 time to fit residues: 2102.5664 Evaluate side-chains 559 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 540 time to evaluate : 4.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain L residue 94 GLU Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 90 ARG Chi-restraints excluded: chain N residue 90 ARG Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain O residue 90 ARG Chi-restraints excluded: chain P residue 90 ARG Chi-restraints excluded: chain S residue 90 ARG Chi-restraints excluded: chain S residue 116 GLU Chi-restraints excluded: chain U residue 167 GLU Chi-restraints excluded: chain W residue 167 GLU Chi-restraints excluded: chain X residue 90 ARG Chi-restraints excluded: chain X residue 157 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 5.9990 chunk 344 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 298 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 324 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 332 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN C 14 GLN D 14 GLN E 14 GLN F 14 GLN H 14 GLN J 14 GLN K 14 GLN L 14 GLN M 14 GLN N 14 GLN O 7 GLN O 14 GLN Q 14 GLN R 14 GLN U 14 GLN V 14 GLN W 14 GLN X 14 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.122997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.113558 restraints weight = 49180.401| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.08 r_work: 0.3252 rms_B_bonded: 0.99 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 1.64 restraints_weight: 0.2500 r_work: 0.2963 rms_B_bonded: 4.17 restraints_weight: 0.1250 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 34512 Z= 0.349 Angle : 0.609 7.047 46416 Z= 0.332 Chirality : 0.038 0.159 4848 Planarity : 0.005 0.047 6096 Dihedral : 4.712 49.184 4513 Min Nonbonded Distance : 1.531 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.58 % Allowed : 16.42 % Favored : 83.00 % 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: 3.73 (0.12), residues: 4080 helix: 3.08 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.06 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP B 93 HIS 0.005 0.002 HIS K 128 PHE 0.026 0.003 PHE R 41 TYR 0.018 0.002 TYR E 137 ARG 0.005 0.001 ARG X 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28285.72 seconds wall clock time: 484 minutes 18.82 seconds (29058.82 seconds total)