Starting phenix.real_space_refine on Mon Dec 30 22:51:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tu8_41619/12_2024/8tu8_41619.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tu8_41619/12_2024/8tu8_41619.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/8tu8_41619/12_2024/8tu8_41619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tu8_41619/12_2024/8tu8_41619.map" model { file = "/net/cci-nas-00/data/ceres_data/8tu8_41619/12_2024/8tu8_41619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tu8_41619/12_2024/8tu8_41619.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.101 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 6 7.16 5 Zn 24 6.06 5 S 192 5.16 5 C 21216 2.51 5 N 5928 2.21 5 O 6480 1.98 5 H 32400 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 66246 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "B" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "C" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "D" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "E" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "F" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "G" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "H" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "I" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "J" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "K" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "L" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "M" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "N" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "O" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "P" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Q" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "R" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "S" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "T" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "U" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "V" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "W" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "X" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 24.77, per 1000 atoms: 0.37 Number of scatterers: 66246 At special positions: 0 Unit cell: (131.37, 131.37, 133.11, 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: 14.36 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 202 " pdb="ZN ZN A 202 " - pdb=" ND1 HIS A 65 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" ND1 HIS B 65 " pdb=" ZN C 202 " pdb="ZN ZN C 202 " - pdb=" ND1 HIS C 65 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" ND1 HIS D 65 " pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" ND1 HIS E 65 " pdb=" ZN F 201 " pdb="ZN ZN F 201 " - pdb=" ND1 HIS F 65 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" ND1 HIS G 65 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" ND1 HIS H 65 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" ND1 HIS I 65 " pdb=" ZN J 201 " pdb="ZN ZN J 201 " - pdb=" ND1 HIS J 65 " pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" ND1 HIS K 65 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" ND1 HIS L 65 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" ND1 HIS M 65 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" ND1 HIS N 65 " pdb=" ZN O 201 " pdb="ZN ZN O 201 " - pdb=" ND1 HIS O 65 " pdb=" ZN P 201 " pdb="ZN ZN P 201 " - pdb=" ND1 HIS P 65 " pdb=" ZN Q 202 " pdb="ZN ZN Q 202 " - pdb=" ND1 HIS Q 65 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 65 " pdb=" ZN S 201 " pdb="ZN ZN S 201 " - pdb=" ND1 HIS S 65 " pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" ND1 HIS T 65 " pdb=" ZN U 201 " pdb="ZN ZN U 201 " - pdb=" ND1 HIS U 65 " pdb=" ZN V 201 " pdb="ZN ZN V 201 " - pdb=" ND1 HIS V 65 " pdb=" ZN W 201 " pdb="ZN ZN W 201 " - pdb=" ND1 HIS W 65 " pdb=" ZN X 201 " pdb="ZN ZN X 201 " - pdb=" ND1 HIS X 65 " 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.08 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 158 Processing helix chain 'A' and resid 163 through 174 removed outlier: 3.998A pdb=" N GLU A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.905A 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: 4.018A pdb=" N GLU B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 3.919A 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: 4.020A pdb=" N GLU C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.022A 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: 4.016A pdb=" N GLU D 167 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 76 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 163 through 174 removed outlier: 4.132A pdb=" N GLU E 167 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 4.094A 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: 4.041A pdb=" N GLU F 167 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 4.077A 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: 4.051A pdb=" N GLU G 167 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 4.019A 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: 4.066A pdb=" N GLU H 167 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 4.037A 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: 4.091A pdb=" N GLU I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 4.062A 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: 4.031A pdb=" N GLU J 167 " --> pdb=" O ALA J 163 " (cutoff:3.500A) removed outlier: 4.062A 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: 3.987A pdb=" N GLU K 167 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 3.977A 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: 4.072A pdb=" N GLU L 167 " --> pdb=" O ALA L 163 " (cutoff:3.500A) removed outlier: 4.090A 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: 4.018A pdb=" N GLU M 167 " --> pdb=" O ALA M 163 " (cutoff:3.500A) removed outlier: 4.029A 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: 4.056A pdb=" N GLU N 167 " --> pdb=" O ALA N 163 " (cutoff:3.500A) removed outlier: 3.933A 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: 4.107A pdb=" N GLU O 167 " --> pdb=" O ALA O 163 " (cutoff:3.500A) removed outlier: 4.109A 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: 4.037A pdb=" N GLU P 167 " --> pdb=" O ALA P 163 " (cutoff:3.500A) removed outlier: 4.016A 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: 4.012A pdb=" N GLU Q 167 " --> pdb=" O ALA Q 163 " (cutoff:3.500A) removed outlier: 3.973A 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: 4.028A pdb=" N GLU R 167 " --> pdb=" O ALA R 163 " (cutoff:3.500A) removed outlier: 3.984A 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: 4.092A pdb=" N GLU S 167 " --> pdb=" O ALA S 163 " (cutoff:3.500A) removed outlier: 4.063A 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: 4.033A pdb=" N GLU T 167 " --> pdb=" O ALA T 163 " (cutoff:3.500A) removed outlier: 4.047A 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: 4.072A pdb=" N GLU U 167 " --> pdb=" O ALA U 163 " (cutoff:3.500A) removed outlier: 4.051A 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: 4.070A pdb=" N GLU V 167 " --> pdb=" O ALA V 163 " (cutoff:3.500A) removed outlier: 4.052A 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: 4.098A pdb=" N GLU W 167 " --> pdb=" O ALA W 163 " (cutoff:3.500A) removed outlier: 4.088A 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: 4.073A pdb=" N GLU X 167 " --> pdb=" O ALA X 163 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR X 168 " --> pdb=" O GLY X 164 " (cutoff:3.500A) 2639 hydrogen bonds defined for protein. 7917 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: 22.35 Time building geometry restraints manager: 17.25 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: 347 1.23 - 1.42: 14701 1.42 - 1.62: 19224 1.62 - 1.81: 312 Bond restraints: 66912 Sorted by residual: bond pdb=" CG1 ILE L 24 " pdb=" CD1 ILE L 24 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.03e+00 bond pdb=" CG GLU G 107 " pdb=" CD GLU G 107 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.25e+00 bond pdb=" CG GLU N 107 " pdb=" CD GLU N 107 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.13e+00 bond pdb=" CG GLU W 107 " pdb=" CD GLU W 107 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.04e+00 bond pdb=" CD1 TYR W 34 " pdb=" CE1 TYR W 34 " ideal model delta sigma weight residual 1.382 1.351 0.031 3.00e-02 1.11e+03 1.04e+00 ... (remaining 66907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 116448 1.38 - 2.76: 3531 2.76 - 4.15: 258 4.15 - 5.53: 51 5.53 - 6.91: 24 Bond angle restraints: 120312 Sorted by residual: angle pdb=" C TRP P 93 " pdb=" N GLU P 94 " pdb=" CA GLU P 94 " ideal model delta sigma weight residual 121.54 127.90 -6.36 1.91e+00 2.74e-01 1.11e+01 angle pdb=" C TRP M 93 " pdb=" N GLU M 94 " pdb=" CA GLU M 94 " ideal model delta sigma weight residual 121.54 127.77 -6.23 1.91e+00 2.74e-01 1.06e+01 angle pdb=" C TRP Q 93 " pdb=" N GLU Q 94 " pdb=" CA GLU Q 94 " ideal model delta sigma weight residual 121.54 127.68 -6.14 1.91e+00 2.74e-01 1.03e+01 angle pdb=" C TRP E 93 " pdb=" N GLU E 94 " pdb=" CA GLU E 94 " ideal model delta sigma weight residual 121.54 127.68 -6.14 1.91e+00 2.74e-01 1.03e+01 angle pdb=" C TRP X 93 " pdb=" N GLU X 94 " pdb=" CA GLU X 94 " ideal model delta sigma weight residual 121.54 127.63 -6.09 1.91e+00 2.74e-01 1.02e+01 ... (remaining 120307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 27961 18.00 - 36.00: 2491 36.00 - 54.00: 664 54.00 - 71.99: 266 71.99 - 89.99: 178 Dihedral angle restraints: 31560 sinusoidal: 16920 harmonic: 14640 Sorted by residual: 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 180.00 158.88 21.12 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA TRP B 93 " pdb=" C TRP B 93 " pdb=" N GLU B 94 " pdb=" CA GLU B 94 " ideal model delta harmonic sigma weight residual 180.00 159.47 20.53 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA TRP O 93 " pdb=" C TRP O 93 " pdb=" N GLU O 94 " pdb=" CA GLU O 94 " ideal model delta harmonic sigma weight residual 180.00 159.51 20.49 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 31557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2991 0.025 - 0.051: 1280 0.051 - 0.076: 354 0.076 - 0.101: 127 0.101 - 0.126: 96 Chirality restraints: 4848 Sorted by residual: chirality pdb=" CA GLU O 94 " pdb=" N GLU O 94 " pdb=" C GLU O 94 " pdb=" CB GLU O 94 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA PRO G 127 " pdb=" N PRO G 127 " pdb=" C PRO G 127 " pdb=" CB PRO G 127 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA PRO R 127 " pdb=" N PRO R 127 " pdb=" C PRO R 127 " pdb=" CB PRO R 127 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 4845 not shown) Planarity restraints: 10128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP E 93 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C TRP E 93 " -0.024 2.00e-02 2.50e+03 pdb=" O TRP E 93 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU E 94 " 0.008 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 1.36e-02 1.86e+00 pdb=" C TRP D 93 " 0.024 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 delta sigma weight rms_deltas residual plane pdb=" CA TRP L 93 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C TRP L 93 " 0.023 2.00e-02 2.50e+03 pdb=" O TRP L 93 " -0.009 2.00e-02 2.50e+03 pdb=" N GLU L 94 " -0.008 2.00e-02 2.50e+03 ... (remaining 10125 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 4114 2.18 - 2.79: 137480 2.79 - 3.39: 219428 3.39 - 4.00: 284971 4.00 - 4.60: 430904 Nonbonded interactions: 1076897 Sorted by model distance: nonbonded pdb=" CD2 HIS H 65 " pdb="ZN ZN H 201 " model vdw 1.579 1.968 nonbonded pdb=" CD2 HIS W 65 " pdb="ZN ZN W 201 " model vdw 1.580 1.968 nonbonded pdb=" CD2 HIS Q 65 " pdb="ZN ZN Q 202 " model vdw 1.584 1.968 nonbonded pdb=" HB3 HIS H 65 " pdb="ZN ZN H 201 " model vdw 1.588 1.930 nonbonded pdb=" HB3 HIS Q 65 " pdb="ZN ZN Q 202 " model vdw 1.588 1.930 ... (remaining 1076892 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.880 Extract box with map and model: 2.120 Check model and map are aligned: 0.390 Set scattering table: 0.490 Process input model: 132.780 Find NCS groups from input model: 2.540 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 34512 Z= 0.269 Angle : 0.574 6.910 46416 Z= 0.314 Chirality : 0.035 0.126 4848 Planarity : 0.004 0.028 6096 Dihedral : 18.540 89.992 13080 Min Nonbonded Distance : 1.579 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.82 % Allowed : 13.93 % Favored : 85.25 % 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: 4.55 (0.13), residues: 4080 helix: 3.58 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.67 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP S 93 HIS 0.005 0.001 HIS B 128 PHE 0.017 0.002 PHE N 41 TYR 0.012 0.002 TYR L 137 ARG 0.004 0.001 ARG E 9 *********************** 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 638 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 608 time to evaluate : 4.252 Fit side-chains REVERT: E 71 LYS cc_start: 0.8239 (tttm) cc_final: 0.7715 (ttpp) REVERT: E 94 GLU cc_start: 0.7290 (pt0) cc_final: 0.7078 (pt0) REVERT: G 143 LYS cc_start: 0.7991 (mtmt) cc_final: 0.7595 (tmmt) REVERT: H 124 LYS cc_start: 0.8634 (mmtt) cc_final: 0.8396 (mmtm) REVERT: I 71 LYS cc_start: 0.8269 (tttm) cc_final: 0.7753 (ttpp) REVERT: N 71 LYS cc_start: 0.8237 (tttm) cc_final: 0.7705 (ttpp) REVERT: P 63 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7862 (tmm160) outliers start: 30 outliers final: 26 residues processed: 629 average time/residue: 3.5824 time to fit residues: 2588.4166 Evaluate side-chains 640 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 613 time to evaluate : 4.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 167 GLU Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain L residue 167 GLU Chi-restraints excluded: chain M residue 167 GLU Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 63 ARG Chi-restraints excluded: chain P residue 167 GLU Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain Q residue 167 GLU Chi-restraints excluded: chain R residue 167 GLU Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 167 GLU Chi-restraints excluded: chain W residue 165 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 5.9990 chunk 309 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 208 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 319 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 238 optimal weight: 1.9990 chunk 370 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN B 75 GLN C 75 GLN D 75 GLN E 75 GLN F 75 GLN G 75 GLN H 75 GLN J 75 GLN K 75 GLN L 75 GLN M 75 GLN N 75 GLN O 75 GLN P 75 GLN Q 11 ASN Q 75 GLN S 75 GLN S 98 ASN T 75 GLN U 75 GLN V 11 ASN V 75 GLN W 75 GLN X 75 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.0474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 34512 Z= 0.278 Angle : 0.573 6.147 46416 Z= 0.310 Chirality : 0.035 0.129 4848 Planarity : 0.004 0.051 6096 Dihedral : 6.799 58.623 4584 Min Nonbonded Distance : 1.530 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.15 % Allowed : 13.02 % Favored : 85.83 % 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: 4.52 (0.12), residues: 4080 helix: 3.66 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.26 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP S 93 HIS 0.005 0.001 HIS O 128 PHE 0.018 0.002 PHE N 41 TYR 0.014 0.002 TYR L 137 ARG 0.004 0.001 ARG T 76 *********************** 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 647 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 605 time to evaluate : 4.278 Fit side-chains revert: symmetry clash REVERT: A 167 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7999 (mt-10) REVERT: H 124 LYS cc_start: 0.8662 (mmtt) cc_final: 0.8432 (mmtm) REVERT: J 167 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: M 167 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8002 (mt-10) REVERT: P 63 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7836 (ttm110) REVERT: T 63 ARG cc_start: 0.7769 (tpt90) cc_final: 0.7359 (ttp80) outliers start: 42 outliers final: 12 residues processed: 633 average time/residue: 3.5421 time to fit residues: 2578.8153 Evaluate side-chains 612 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 596 time to evaluate : 4.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain J residue 167 GLU Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain M residue 167 GLU Chi-restraints excluded: chain P residue 63 ARG Chi-restraints excluded: chain Q residue 167 GLU Chi-restraints excluded: chain R residue 167 GLU Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain U residue 165 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 308 optimal weight: 4.9990 chunk 252 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 371 optimal weight: 1.9990 chunk 400 optimal weight: 3.9990 chunk 330 optimal weight: 5.9990 chunk 368 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 297 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 75 GLN D 75 GLN E 65 HIS E 75 GLN G 75 GLN O 75 GLN P 75 GLN Q 75 GLN S 75 GLN U 11 ASN W 11 ASN W 75 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.0543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 34512 Z= 0.273 Angle : 0.565 6.092 46416 Z= 0.306 Chirality : 0.035 0.131 4848 Planarity : 0.004 0.045 6096 Dihedral : 5.350 58.407 4541 Min Nonbonded Distance : 1.550 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.23 % Allowed : 13.35 % Favored : 85.42 % 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: 4.53 (0.13), residues: 4080 helix: 3.68 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.20 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP B 93 HIS 0.005 0.001 HIS E 128 PHE 0.017 0.002 PHE N 41 TYR 0.015 0.002 TYR K 137 ARG 0.005 0.001 ARG S 90 *********************** 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 647 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 602 time to evaluate : 4.354 Fit side-chains revert: symmetry clash REVERT: H 124 LYS cc_start: 0.8669 (mmtt) cc_final: 0.8444 (mmtm) REVERT: U 94 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7122 (pt0) REVERT: V 94 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.7110 (pt0) REVERT: W 62 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7978 (mm-30) REVERT: X 158 MET cc_start: 0.9096 (mtp) cc_final: 0.8823 (mtp) outliers start: 45 outliers final: 9 residues processed: 628 average time/residue: 3.5048 time to fit residues: 2530.8263 Evaluate side-chains 616 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 605 time to evaluate : 4.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain P residue 63 ARG Chi-restraints excluded: chain U residue 94 GLU Chi-restraints excluded: chain V residue 94 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: 5.9990 chunk 192 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 249 optimal weight: 0.8980 chunk 372 optimal weight: 0.9980 chunk 394 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 353 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS B 11 ASN B 65 HIS C 75 GLN E 111 ASN F 75 GLN G 14 GLN H 75 GLN I 11 ASN J 75 GLN K 14 GLN K 75 GLN M 11 ASN M 75 GLN N 65 HIS Q 75 GLN T 75 GLN U 65 HIS U 98 ASN X 11 ASN X 75 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.0719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34512 Z= 0.200 Angle : 0.515 5.814 46416 Z= 0.277 Chirality : 0.032 0.129 4848 Planarity : 0.004 0.036 6096 Dihedral : 4.439 58.527 4517 Min Nonbonded Distance : 1.633 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.55 % Allowed : 14.53 % Favored : 84.92 % 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: 4.90 (0.13), residues: 4080 helix: 3.96 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.25 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP S 93 HIS 0.004 0.001 HIS C 128 PHE 0.014 0.002 PHE N 41 TYR 0.011 0.001 TYR H 137 ARG 0.003 0.000 ARG S 90 *********************** 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 629 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 609 time to evaluate : 4.463 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7845 (mm-30) REVERT: A 75 GLN cc_start: 0.8254 (mt0) cc_final: 0.8049 (mt0) REVERT: B 62 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7831 (mm-30) REVERT: B 75 GLN cc_start: 0.8279 (mt0) cc_final: 0.8053 (mt0) REVERT: B 143 LYS cc_start: 0.7887 (tmmt) cc_final: 0.7627 (mttm) REVERT: C 75 GLN cc_start: 0.8227 (mt0) cc_final: 0.8014 (mt0) REVERT: E 75 GLN cc_start: 0.8269 (mt0) cc_final: 0.8061 (mt0) REVERT: G 75 GLN cc_start: 0.8258 (mt0) cc_final: 0.8058 (mt0) REVERT: H 75 GLN cc_start: 0.8204 (mt0) cc_final: 0.7996 (mt0) REVERT: H 124 LYS cc_start: 0.8645 (mmtt) cc_final: 0.8423 (mmtm) REVERT: H 143 LYS cc_start: 0.7988 (tmmt) cc_final: 0.7651 (mttt) REVERT: J 75 GLN cc_start: 0.8225 (mt0) cc_final: 0.8024 (mt0) REVERT: K 75 GLN cc_start: 0.8200 (mt0) cc_final: 0.7988 (mt0) REVERT: M 75 GLN cc_start: 0.8223 (mt0) cc_final: 0.8016 (mt0) REVERT: N 75 GLN cc_start: 0.8256 (mt0) cc_final: 0.8056 (mt0) REVERT: O 75 GLN cc_start: 0.8267 (mt0) cc_final: 0.8057 (mt0) REVERT: O 143 LYS cc_start: 0.7994 (tmmt) cc_final: 0.7657 (mttt) REVERT: P 75 GLN cc_start: 0.8272 (mt0) cc_final: 0.8056 (mt0) REVERT: P 143 LYS cc_start: 0.8005 (tmmt) cc_final: 0.7633 (mttt) REVERT: Q 143 LYS cc_start: 0.7985 (tmmt) cc_final: 0.7659 (mttt) REVERT: R 143 LYS cc_start: 0.7927 (tmmt) cc_final: 0.7623 (mttt) REVERT: S 75 GLN cc_start: 0.8270 (mt0) cc_final: 0.8062 (mt0) REVERT: T 75 GLN cc_start: 0.8217 (mt0) cc_final: 0.8013 (mt0) REVERT: U 143 LYS cc_start: 0.7996 (tmmt) cc_final: 0.7666 (mttt) REVERT: V 75 GLN cc_start: 0.8271 (mt0) cc_final: 0.8053 (mt0) REVERT: V 143 LYS cc_start: 0.7995 (tmmt) cc_final: 0.7650 (mttt) REVERT: W 75 GLN cc_start: 0.8259 (mt0) cc_final: 0.8050 (mt0) REVERT: X 75 GLN cc_start: 0.8220 (mt0) cc_final: 0.8003 (mt0) REVERT: X 143 LYS cc_start: 0.7984 (tmmt) cc_final: 0.7647 (mttt) REVERT: X 158 MET cc_start: 0.9083 (mtp) cc_final: 0.8837 (mtp) outliers start: 20 outliers final: 2 residues processed: 627 average time/residue: 3.6047 time to fit residues: 2618.0275 Evaluate side-chains 611 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 609 time to evaluate : 4.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain P residue 63 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 293 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 336 optimal weight: 2.9990 chunk 272 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 201 optimal weight: 6.9990 chunk 353 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 111 ASN F 14 GLN H 14 GLN K 14 GLN L 14 GLN M 14 GLN O 10 GLN Q 14 GLN V 14 GLN W 14 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.0741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 34512 Z= 0.347 Angle : 0.612 6.451 46416 Z= 0.334 Chirality : 0.037 0.137 4848 Planarity : 0.005 0.053 6096 Dihedral : 4.679 57.570 4516 Min Nonbonded Distance : 1.439 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.93 % Allowed : 13.62 % Favored : 85.44 % 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 (0.12), residues: 4080 helix: 3.55 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.06 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 93 HIS 0.006 0.002 HIS Q 57 PHE 0.020 0.003 PHE K 41 TYR 0.016 0.002 TYR L 137 ARG 0.006 0.001 ARG S 9 *********************** 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 613 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 579 time to evaluate : 4.436 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7960 (mm-30) REVERT: B 62 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7963 (mm-30) REVERT: E 63 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7874 (tmm160) REVERT: H 124 LYS cc_start: 0.8650 (mmtt) cc_final: 0.8426 (mmtm) REVERT: K 63 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7870 (tmm160) REVERT: O 63 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7887 (tmm160) REVERT: R 158 MET cc_start: 0.9110 (mtp) cc_final: 0.8889 (mtp) REVERT: X 143 LYS cc_start: 0.8032 (tmmt) cc_final: 0.7714 (mttt) outliers start: 34 outliers final: 12 residues processed: 594 average time/residue: 3.6340 time to fit residues: 2470.4927 Evaluate side-chains 599 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 584 time to evaluate : 4.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain O residue 63 ARG Chi-restraints excluded: chain P residue 63 ARG Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 165 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 5.9990 chunk 355 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 394 optimal weight: 3.9990 chunk 327 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN C 75 GLN D 14 GLN F 14 GLN G 14 GLN H 14 GLN H 75 GLN J 75 GLN K 14 GLN L 14 GLN M 14 GLN M 75 GLN Q 14 GLN R 65 HIS R 75 GLN T 75 GLN V 14 GLN W 14 GLN X 75 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 34512 Z= 0.306 Angle : 0.589 6.526 46416 Z= 0.319 Chirality : 0.036 0.133 4848 Planarity : 0.005 0.050 6096 Dihedral : 4.637 57.931 4516 Min Nonbonded Distance : 1.447 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.90 % Allowed : 14.06 % Favored : 85.03 % 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: 4.38 (0.12), residues: 4080 helix: 3.60 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.01 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP E 93 HIS 0.005 0.001 HIS A 57 PHE 0.018 0.003 PHE N 41 TYR 0.015 0.002 TYR L 137 ARG 0.004 0.001 ARG S 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 622 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 589 time to evaluate : 4.554 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7916 (mm-30) REVERT: B 62 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7914 (mm-30) REVERT: E 63 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7878 (tmm160) REVERT: H 124 LYS cc_start: 0.8668 (mmtt) cc_final: 0.8441 (mmtm) REVERT: H 143 LYS cc_start: 0.8039 (tmmt) cc_final: 0.7634 (mttt) REVERT: O 143 LYS cc_start: 0.8031 (tmmt) cc_final: 0.7607 (mttt) REVERT: X 143 LYS cc_start: 0.8022 (tmmt) cc_final: 0.7709 (mttt) outliers start: 33 outliers final: 14 residues processed: 605 average time/residue: 3.5378 time to fit residues: 2458.5762 Evaluate side-chains 608 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 593 time to evaluate : 4.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain P residue 63 ARG Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain X residue 95 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 224 optimal weight: 2.9990 chunk 288 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 332 optimal weight: 4.9990 chunk 220 optimal weight: 3.9990 chunk 393 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN C 75 GLN D 14 GLN E 14 GLN F 14 GLN G 14 GLN G 75 GLN H 14 GLN H 75 GLN I 14 GLN J 75 GLN K 14 GLN L 14 GLN L 75 GLN M 14 GLN M 75 GLN O 14 GLN O 75 GLN Q 14 GLN R 75 GLN S 14 GLN T 14 GLN T 75 GLN V 14 GLN W 14 GLN X 75 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 34512 Z= 0.324 Angle : 0.609 6.585 46416 Z= 0.330 Chirality : 0.037 0.135 4848 Planarity : 0.005 0.054 6096 Dihedral : 4.681 57.718 4516 Min Nonbonded Distance : 1.491 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.90 % Allowed : 14.12 % Favored : 84.98 % 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: 4.28 (0.12), residues: 4080 helix: 3.47 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 0.13 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 93 HIS 0.005 0.002 HIS A 57 PHE 0.019 0.003 PHE N 41 TYR 0.015 0.002 TYR R 137 ARG 0.005 0.001 ARG U 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 624 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 591 time to evaluate : 4.280 Fit side-chains REVERT: I 71 LYS cc_start: 0.8286 (tttm) cc_final: 0.7778 (ttpp) REVERT: K 124 LYS cc_start: 0.8651 (mmtt) cc_final: 0.8428 (mmtm) REVERT: O 143 LYS cc_start: 0.8052 (tmmt) cc_final: 0.7638 (mttt) REVERT: X 143 LYS cc_start: 0.8054 (tmmt) cc_final: 0.7721 (mttt) outliers start: 33 outliers final: 14 residues processed: 608 average time/residue: 3.6159 time to fit residues: 2518.3823 Evaluate side-chains 592 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 578 time to evaluate : 4.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain P residue 63 ARG Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 95 SER Chi-restraints excluded: chain X residue 165 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 234 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 250 optimal weight: 3.9990 chunk 267 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 309 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN C 75 GLN D 14 GLN E 14 GLN E 75 GLN F 14 GLN G 14 GLN G 75 GLN H 14 GLN H 75 GLN I 14 GLN I 75 GLN J 75 GLN K 14 GLN K 75 GLN L 14 GLN L 75 GLN M 14 GLN M 75 GLN O 14 GLN O 75 GLN P 75 GLN Q 14 GLN R 75 GLN S 14 GLN S 75 GLN T 14 GLN T 75 GLN U 14 GLN V 14 GLN W 14 GLN X 75 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 34512 Z= 0.335 Angle : 0.615 6.886 46416 Z= 0.333 Chirality : 0.037 0.134 4848 Planarity : 0.005 0.055 6096 Dihedral : 4.707 57.700 4516 Min Nonbonded Distance : 1.484 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.77 % Allowed : 14.31 % Favored : 84.92 % 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: 4.24 (0.12), residues: 4080 helix: 3.45 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 0.07 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 93 HIS 0.005 0.002 HIS A 57 PHE 0.019 0.003 PHE R 41 TYR 0.015 0.002 TYR L 137 ARG 0.005 0.001 ARG S 9 *********************** 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 615 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 587 time to evaluate : 4.256 Fit side-chains REVERT: I 71 LYS cc_start: 0.8289 (tttm) cc_final: 0.7779 (ttpp) REVERT: K 124 LYS cc_start: 0.8653 (mmtt) cc_final: 0.8430 (mmtm) REVERT: X 143 LYS cc_start: 0.8055 (tmmt) cc_final: 0.7720 (mttt) outliers start: 28 outliers final: 12 residues processed: 602 average time/residue: 3.6319 time to fit residues: 2505.3949 Evaluate side-chains 589 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 577 time to evaluate : 4.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain P residue 63 ARG Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain X residue 95 SER 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: 4.9990 chunk 366 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 287 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 331 optimal weight: 0.7980 chunk 346 optimal weight: 3.9990 chunk 365 optimal weight: 0.1980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN D 11 ASN D 14 GLN E 14 GLN E 75 GLN F 14 GLN G 14 GLN G 75 GLN H 14 GLN H 75 GLN I 14 GLN I 75 GLN J 75 GLN K 14 GLN K 75 GLN L 14 GLN L 75 GLN M 14 GLN M 75 GLN N 11 ASN N 75 GLN O 14 GLN O 75 GLN P 75 GLN Q 14 GLN R 11 ASN R 75 GLN S 14 GLN T 11 ASN T 14 GLN T 75 GLN U 14 GLN V 14 GLN W 14 GLN W 75 GLN X 75 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34512 Z= 0.216 Angle : 0.546 6.445 46416 Z= 0.292 Chirality : 0.033 0.124 4848 Planarity : 0.004 0.043 6096 Dihedral : 4.459 58.623 4516 Min Nonbonded Distance : 1.626 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.27 % Allowed : 14.88 % Favored : 84.84 % 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: 4.74 (0.13), residues: 4080 helix: 3.87 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.09 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP S 93 HIS 0.004 0.001 HIS K 128 PHE 0.015 0.002 PHE E 41 TYR 0.011 0.002 TYR H 137 ARG 0.003 0.000 ARG U 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 617 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 607 time to evaluate : 4.277 Fit side-chains REVERT: A 75 GLN cc_start: 0.8192 (mt0) cc_final: 0.7986 (mt0) REVERT: B 75 GLN cc_start: 0.8281 (mt0) cc_final: 0.8060 (mt0) REVERT: G 75 GLN cc_start: 0.8205 (mt0) cc_final: 0.8003 (mt0) REVERT: H 75 GLN cc_start: 0.8208 (mt0) cc_final: 0.8002 (mt0) REVERT: I 71 LYS cc_start: 0.8282 (tttm) cc_final: 0.7741 (ttpp) REVERT: I 75 GLN cc_start: 0.8235 (mt0) cc_final: 0.8013 (mt0) REVERT: K 75 GLN cc_start: 0.8191 (mt0) cc_final: 0.7981 (mt0) REVERT: N 62 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7842 (mm-30) REVERT: N 75 GLN cc_start: 0.8239 (mt0) cc_final: 0.8012 (mt0) REVERT: O 75 GLN cc_start: 0.8183 (mt0) cc_final: 0.7982 (mt0) REVERT: O 143 LYS cc_start: 0.8023 (tmmt) cc_final: 0.7704 (mtmt) REVERT: P 75 GLN cc_start: 0.8220 (mt0) cc_final: 0.8011 (mt0) REVERT: P 143 LYS cc_start: 0.8029 (tmmt) cc_final: 0.7676 (mttm) REVERT: Q 143 LYS cc_start: 0.8015 (tmmt) cc_final: 0.7657 (mttm) REVERT: R 75 GLN cc_start: 0.8189 (mt0) cc_final: 0.7983 (mt0) REVERT: U 143 LYS cc_start: 0.8004 (tmmt) cc_final: 0.7666 (mttm) REVERT: V 143 LYS cc_start: 0.8023 (tmmt) cc_final: 0.7669 (mttm) REVERT: W 75 GLN cc_start: 0.8219 (mt0) cc_final: 0.8005 (mt0) REVERT: X 75 GLN cc_start: 0.8214 (mt0) cc_final: 0.8001 (mt0) REVERT: X 143 LYS cc_start: 0.7990 (tmmt) cc_final: 0.7637 (mttt) outliers start: 10 outliers final: 2 residues processed: 617 average time/residue: 3.5433 time to fit residues: 2510.0558 Evaluate side-chains 605 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 603 time to evaluate : 4.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain P residue 63 ARG 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: 0.8980 chunk 236 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 269 optimal weight: 5.9990 chunk 406 optimal weight: 6.9990 chunk 374 optimal weight: 5.9990 chunk 323 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 250 optimal weight: 0.0870 chunk 198 optimal weight: 5.9990 overall best weight: 2.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN D 14 GLN E 14 GLN F 14 GLN G 14 GLN H 14 GLN I 14 GLN K 14 GLN L 14 GLN M 14 GLN O 14 GLN Q 14 GLN S 14 GLN T 14 GLN U 14 GLN V 14 GLN W 14 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 34512 Z= 0.273 Angle : 0.582 7.011 46416 Z= 0.314 Chirality : 0.035 0.131 4848 Planarity : 0.004 0.046 6096 Dihedral : 4.571 57.754 4516 Min Nonbonded Distance : 1.513 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.16 % Allowed : 15.10 % Favored : 84.73 % 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: 4.51 (0.13), residues: 4080 helix: 3.63 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 0.22 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP O 93 HIS 0.004 0.001 HIS Q 57 PHE 0.018 0.002 PHE E 41 TYR 0.014 0.002 TYR I 137 ARG 0.004 0.001 ARG U 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 586 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 580 time to evaluate : 4.316 Fit side-chains REVERT: D 143 LYS cc_start: 0.7984 (mtmt) cc_final: 0.7601 (tmmt) REVERT: G 143 LYS cc_start: 0.7985 (mtmt) cc_final: 0.7602 (tmmt) REVERT: I 71 LYS cc_start: 0.8286 (tttm) cc_final: 0.7776 (ttpp) REVERT: K 158 MET cc_start: 0.9086 (mtp) cc_final: 0.8861 (mtp) REVERT: N 75 GLN cc_start: 0.8276 (mt0) cc_final: 0.8064 (mt0) REVERT: Q 143 LYS cc_start: 0.8034 (tmmt) cc_final: 0.7611 (mttt) REVERT: V 143 LYS cc_start: 0.8043 (tmmt) cc_final: 0.7628 (mttt) outliers start: 6 outliers final: 2 residues processed: 585 average time/residue: 3.6454 time to fit residues: 2440.6713 Evaluate side-chains 576 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 574 time to evaluate : 4.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain P residue 63 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 4.9990 chunk 344 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 298 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 324 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 332 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 59 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 14 GLN F 14 GLN G 14 GLN H 14 GLN I 14 GLN K 14 GLN L 14 GLN M 14 GLN O 14 GLN Q 14 GLN S 14 GLN T 14 GLN U 14 GLN V 14 GLN W 14 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.120501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.111163 restraints weight = 53334.015| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.09 r_work: 0.3195 rms_B_bonded: 0.95 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 1.60 restraints_weight: 0.2500 r_work: 0.2877 rms_B_bonded: 4.12 restraints_weight: 0.1250 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 34512 Z= 0.300 Angle : 0.594 6.791 46416 Z= 0.321 Chirality : 0.036 0.131 4848 Planarity : 0.004 0.048 6096 Dihedral : 4.623 57.750 4516 Min Nonbonded Distance : 1.525 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.19 % Allowed : 15.02 % Favored : 84.79 % 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: 4.41 (0.13), residues: 4080 helix: 3.57 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 0.17 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 93 HIS 0.005 0.001 HIS B 57 PHE 0.018 0.003 PHE E 41 TYR 0.014 0.002 TYR I 137 ARG 0.004 0.001 ARG U 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31443.37 seconds wall clock time: 537 minutes 31.56 seconds (32251.56 seconds total)