Starting phenix.real_space_refine on Thu Feb 5 11:43:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k82_62158/02_2026/9k82_62158.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k82_62158/02_2026/9k82_62158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k82_62158/02_2026/9k82_62158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k82_62158/02_2026/9k82_62158.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k82_62158/02_2026/9k82_62158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k82_62158/02_2026/9k82_62158.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.012 sd= 0.161 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: 5 Type Number sf(0) Gaussians Zn 24 6.06 5 S 24 5.16 5 C 10716 2.51 5 N 3108 2.21 5 O 3204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17076 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1421 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 175} Chain: "B" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1421 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 175} Chain: "C" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1421 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 175} Chain: "D" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1421 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 175} Chain: "E" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1421 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 175} Chain: "F" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1421 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 175} Chain: "G" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1421 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 175} Chain: "H" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1421 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 175} Chain: "I" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1421 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 175} Chain: "J" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1421 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 175} Chain: "K" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1421 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 175} Chain: "L" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1421 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 175} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} 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: {' ZN': 2} 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: {' ZN': 2} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.69, per 1000 atoms: 0.22 Number of scatterers: 17076 At special positions: 0 Unit cell: (91.5705, 89.4159, 188.528, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 24 29.99 S 24 16.00 O 3204 8.00 N 3108 7.00 C 10716 6.00 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: 1.33 Conformation dependent library (CDL) restraints added in 603.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" NE2 HIS B 100 " pdb="ZN ZN A 201 " - pdb=" NE2 HIS A 23 " pdb=" ZN A 202 " pdb="ZN ZN A 202 " - pdb=" NE2 HIS C 23 " pdb="ZN ZN A 202 " - pdb=" NE2 HIS A 100 " pdb=" ZN A 203 " pdb="ZN ZN A 203 " - pdb=" NE2 HIS A 174 " pdb="ZN ZN A 203 " - pdb=" NE2 HIS I 13 " pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" NE2 HIS D 100 " pdb="ZN ZN B 201 " - pdb=" NE2 HIS B 23 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" NE2 HIS B 174 " pdb="ZN ZN B 202 " - pdb=" NE2 HIS G 13 " pdb=" ZN C 201 " pdb="ZN ZN C 201 " - pdb=" NE2 HIS C 100 " pdb="ZN ZN C 201 " - pdb=" NE2 HIS E 23 " pdb=" ZN C 202 " pdb="ZN ZN C 202 " - pdb=" NE2 HIS C 174 " pdb="ZN ZN C 202 " - pdb=" NE2 HIS K 13 " pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" NE2 HIS F 100 " pdb="ZN ZN D 201 " - pdb=" NE2 HIS D 23 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" NE2 HIS D 174 " pdb="ZN ZN D 202 " - pdb=" NE2 HIS E 13 " pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" NE2 HIS E 100 " pdb="ZN ZN E 201 " - pdb=" NE2 HIS G 23 " pdb=" ZN F 201 " pdb="ZN ZN F 201 " - pdb=" NE2 HIS F 174 " pdb="ZN ZN F 201 " - pdb=" NE2 HIS C 13 " pdb=" ZN F 202 " pdb="ZN ZN F 202 " - pdb=" NE2 HIS F 13 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" NE2 HIS G 100 " pdb="ZN ZN G 201 " - pdb=" NE2 HIS I 23 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" NE2 HIS H 174 " pdb="ZN ZN H 201 " - pdb=" NE2 HIS A 13 " pdb=" ZN H 202 " pdb="ZN ZN H 202 " - pdb=" NE2 HIS H 100 " pdb="ZN ZN H 202 " - pdb=" NE2 HIS F 23 " pdb=" ZN H 203 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 13 " pdb=" ZN H 204 " pdb="ZN ZN H 204 " - pdb=" NE2 HIS J 100 " pdb="ZN ZN H 204 " - pdb=" NE2 HIS H 23 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" NE2 HIS I 100 " pdb="ZN ZN I 201 " - pdb=" NE2 HIS K 23 " pdb=" ZN J 201 " pdb="ZN ZN J 201 " - pdb=" NE2 HIS J 174 " pdb="ZN ZN J 201 " - pdb=" NE2 HIS B 13 " pdb=" ZN J 202 " pdb="ZN ZN J 202 " - pdb=" NE2 HIS J 13 " pdb=" ZN J 203 " pdb="ZN ZN J 203 " - pdb=" NE2 HIS L 100 " pdb="ZN ZN J 203 " - pdb=" NE2 HIS J 23 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" NE2 HIS L 174 " pdb="ZN ZN L 201 " - pdb=" NE2 HIS D 13 " pdb=" ZN L 202 " pdb="ZN ZN L 202 " - pdb=" NE2 HIS L 13 " pdb=" ZN L 203 " pdb="ZN ZN L 203 " - pdb=" NE2 HIS L 23 " 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4344 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 0 sheets defined 92.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 6 through 29 Processing helix chain 'A' and resid 31 through 49 Processing helix chain 'A' and resid 52 through 76 removed outlier: 3.712A pdb=" N GLY A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 96 Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 99 through 122 removed outlier: 3.744A pdb=" N ARG A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A 121 " --> pdb=" O MET A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 143 removed outlier: 3.680A pdb=" N TYR A 129 " --> pdb=" O PRO A 125 " (cutoff:3.500A) Proline residue: A 131 - end of helix Processing helix chain 'A' and resid 146 through 170 removed outlier: 3.539A pdb=" N GLY A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 190 removed outlier: 3.945A pdb=" N THR A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 29 Processing helix chain 'B' and resid 31 through 49 Processing helix chain 'B' and resid 52 through 76 removed outlier: 3.503A pdb=" N GLN B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 96 Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 99 through 122 removed outlier: 3.720A pdb=" N ARG B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA B 121 " --> pdb=" O MET B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 143 removed outlier: 3.660A pdb=" N TYR B 129 " --> pdb=" O PRO B 125 " (cutoff:3.500A) Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 146 through 170 removed outlier: 3.502A pdb=" N ARG B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 190 removed outlier: 3.840A pdb=" N THR B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 29 Processing helix chain 'C' and resid 31 through 49 Processing helix chain 'C' and resid 52 through 76 removed outlier: 3.699A pdb=" N GLY C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 96 Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 99 through 122 removed outlier: 3.683A pdb=" N ARG C 120 " --> pdb=" O ALA C 116 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA C 121 " --> pdb=" O MET C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 143 removed outlier: 3.624A pdb=" N TYR C 129 " --> pdb=" O PRO C 125 " (cutoff:3.500A) Proline residue: C 131 - end of helix Processing helix chain 'C' and resid 146 through 170 removed outlier: 3.507A pdb=" N GLY C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 190 removed outlier: 3.848A pdb=" N THR C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 29 Processing helix chain 'D' and resid 31 through 49 Processing helix chain 'D' and resid 52 through 76 removed outlier: 3.703A pdb=" N GLY D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 96 Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 99 through 122 removed outlier: 3.843A pdb=" N ARG D 120 " --> pdb=" O ALA D 116 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA D 121 " --> pdb=" O MET D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 143 removed outlier: 3.682A pdb=" N TYR D 129 " --> pdb=" O PRO D 125 " (cutoff:3.500A) Proline residue: D 131 - end of helix Processing helix chain 'D' and resid 146 through 170 removed outlier: 3.561A pdb=" N GLY D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 190 removed outlier: 3.977A pdb=" N THR D 189 " --> pdb=" O ARG D 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 29 Processing helix chain 'E' and resid 31 through 49 Processing helix chain 'E' and resid 52 through 76 removed outlier: 3.698A pdb=" N GLY E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 96 removed outlier: 3.521A pdb=" N VAL E 82 " --> pdb=" O PRO E 78 " (cutoff:3.500A) Proline residue: E 84 - end of helix Processing helix chain 'E' and resid 99 through 122 removed outlier: 3.714A pdb=" N ARG E 120 " --> pdb=" O ALA E 116 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA E 121 " --> pdb=" O MET E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 143 removed outlier: 3.662A pdb=" N TYR E 129 " --> pdb=" O PRO E 125 " (cutoff:3.500A) Proline residue: E 131 - end of helix Processing helix chain 'E' and resid 146 through 170 removed outlier: 3.558A pdb=" N GLY E 170 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 190 removed outlier: 3.897A pdb=" N THR E 189 " --> pdb=" O ARG E 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 29 Processing helix chain 'F' and resid 31 through 49 Processing helix chain 'F' and resid 52 through 76 removed outlier: 3.708A pdb=" N GLY F 70 " --> pdb=" O ALA F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 96 Proline residue: F 84 - end of helix Processing helix chain 'F' and resid 99 through 122 removed outlier: 3.755A pdb=" N ARG F 120 " --> pdb=" O ALA F 116 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA F 121 " --> pdb=" O MET F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 143 removed outlier: 3.655A pdb=" N TYR F 129 " --> pdb=" O PRO F 125 " (cutoff:3.500A) Proline residue: F 131 - end of helix Processing helix chain 'F' and resid 146 through 170 removed outlier: 3.502A pdb=" N ARG F 150 " --> pdb=" O ASN F 146 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY F 170 " --> pdb=" O LEU F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 190 removed outlier: 3.884A pdb=" N THR F 189 " --> pdb=" O ARG F 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 29 Processing helix chain 'G' and resid 31 through 49 Processing helix chain 'G' and resid 52 through 76 removed outlier: 3.507A pdb=" N GLN G 56 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY G 70 " --> pdb=" O ALA G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 96 removed outlier: 3.545A pdb=" N VAL G 82 " --> pdb=" O PRO G 78 " (cutoff:3.500A) Proline residue: G 84 - end of helix Processing helix chain 'G' and resid 99 through 122 removed outlier: 3.708A pdb=" N ARG G 120 " --> pdb=" O ALA G 116 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA G 121 " --> pdb=" O MET G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 143 removed outlier: 3.693A pdb=" N TYR G 129 " --> pdb=" O PRO G 125 " (cutoff:3.500A) Proline residue: G 131 - end of helix Processing helix chain 'G' and resid 146 through 170 Processing helix chain 'G' and resid 172 through 190 removed outlier: 3.868A pdb=" N THR G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 29 Processing helix chain 'H' and resid 31 through 49 Processing helix chain 'H' and resid 52 through 76 removed outlier: 3.712A pdb=" N GLY H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 96 removed outlier: 3.506A pdb=" N VAL H 82 " --> pdb=" O PRO H 78 " (cutoff:3.500A) Proline residue: H 84 - end of helix Processing helix chain 'H' and resid 99 through 122 removed outlier: 3.760A pdb=" N ARG H 120 " --> pdb=" O ALA H 116 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA H 121 " --> pdb=" O MET H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 143 removed outlier: 3.652A pdb=" N TYR H 129 " --> pdb=" O PRO H 125 " (cutoff:3.500A) Proline residue: H 131 - end of helix Processing helix chain 'H' and resid 146 through 170 removed outlier: 3.521A pdb=" N GLY H 170 " --> pdb=" O LEU H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 190 removed outlier: 3.960A pdb=" N THR H 189 " --> pdb=" O ARG H 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 29 Processing helix chain 'I' and resid 31 through 49 Processing helix chain 'I' and resid 52 through 76 removed outlier: 3.523A pdb=" N GLN I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY I 70 " --> pdb=" O ALA I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 96 Proline residue: I 84 - end of helix Processing helix chain 'I' and resid 99 through 122 removed outlier: 3.657A pdb=" N ARG I 120 " --> pdb=" O ALA I 116 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA I 121 " --> pdb=" O MET I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 143 removed outlier: 3.637A pdb=" N TYR I 129 " --> pdb=" O PRO I 125 " (cutoff:3.500A) Proline residue: I 131 - end of helix Processing helix chain 'I' and resid 146 through 170 removed outlier: 3.538A pdb=" N ARG I 150 " --> pdb=" O ASN I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 190 removed outlier: 3.879A pdb=" N THR I 189 " --> pdb=" O ARG I 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 29 Processing helix chain 'J' and resid 31 through 49 Processing helix chain 'J' and resid 52 through 76 removed outlier: 3.538A pdb=" N GLN J 56 " --> pdb=" O ASP J 52 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 96 Proline residue: J 84 - end of helix Processing helix chain 'J' and resid 99 through 122 removed outlier: 3.737A pdb=" N ARG J 120 " --> pdb=" O ALA J 116 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA J 121 " --> pdb=" O MET J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 143 removed outlier: 3.660A pdb=" N TYR J 129 " --> pdb=" O PRO J 125 " (cutoff:3.500A) Proline residue: J 131 - end of helix Processing helix chain 'J' and resid 146 through 170 removed outlier: 3.509A pdb=" N ARG J 150 " --> pdb=" O ASN J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 190 removed outlier: 3.769A pdb=" N THR J 189 " --> pdb=" O ARG J 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 29 Processing helix chain 'K' and resid 31 through 49 Processing helix chain 'K' and resid 52 through 76 removed outlier: 3.652A pdb=" N GLN K 56 " --> pdb=" O ASP K 52 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY K 70 " --> pdb=" O ALA K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 96 Proline residue: K 84 - end of helix Processing helix chain 'K' and resid 99 through 122 removed outlier: 3.707A pdb=" N ARG K 120 " --> pdb=" O ALA K 116 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA K 121 " --> pdb=" O MET K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 143 removed outlier: 3.668A pdb=" N TYR K 129 " --> pdb=" O PRO K 125 " (cutoff:3.500A) Proline residue: K 131 - end of helix Processing helix chain 'K' and resid 146 through 170 removed outlier: 3.532A pdb=" N ARG K 150 " --> pdb=" O ASN K 146 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY K 170 " --> pdb=" O LEU K 166 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 190 removed outlier: 3.913A pdb=" N THR K 189 " --> pdb=" O ARG K 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 29 Processing helix chain 'L' and resid 31 through 49 Processing helix chain 'L' and resid 52 through 76 removed outlier: 3.506A pdb=" N GLN L 56 " --> pdb=" O ASP L 52 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY L 70 " --> pdb=" O ALA L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 96 removed outlier: 3.502A pdb=" N VAL L 82 " --> pdb=" O PRO L 78 " (cutoff:3.500A) Proline residue: L 84 - end of helix Processing helix chain 'L' and resid 99 through 122 removed outlier: 3.679A pdb=" N ARG L 120 " --> pdb=" O ALA L 116 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA L 121 " --> pdb=" O MET L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 143 removed outlier: 3.622A pdb=" N TYR L 129 " --> pdb=" O PRO L 125 " (cutoff:3.500A) Proline residue: L 131 - end of helix Processing helix chain 'L' and resid 146 through 170 removed outlier: 3.540A pdb=" N GLY L 170 " --> pdb=" O LEU L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 190 removed outlier: 3.918A pdb=" N THR L 189 " --> pdb=" O ARG L 185 " (cutoff:3.500A) 1538 hydrogen bonds defined for protein. 4614 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: 2.66 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6057 1.34 - 1.45: 666 1.45 - 1.57: 10496 1.57 - 1.69: 1 1.69 - 1.81: 48 Bond restraints: 17268 Sorted by residual: bond pdb=" CG PRO D 191 " pdb=" CD PRO D 191 " ideal model delta sigma weight residual 1.503 1.433 0.070 3.40e-02 8.65e+02 4.23e+00 bond pdb=" CA HIS C 23 " pdb=" C HIS C 23 " ideal model delta sigma weight residual 1.524 1.501 0.023 1.27e-02 6.20e+03 3.28e+00 bond pdb=" CB PRO D 191 " pdb=" CG PRO D 191 " ideal model delta sigma weight residual 1.492 1.574 -0.082 5.00e-02 4.00e+02 2.67e+00 bond pdb=" C HIS C 23 " pdb=" O HIS C 23 " ideal model delta sigma weight residual 1.236 1.220 0.017 1.15e-02 7.56e+03 2.11e+00 bond pdb=" C HIS L 23 " pdb=" O HIS L 23 " ideal model delta sigma weight residual 1.236 1.220 0.016 1.15e-02 7.56e+03 1.99e+00 ... (remaining 17263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 23172 1.64 - 3.27: 345 3.27 - 4.91: 56 4.91 - 6.54: 3 6.54 - 8.18: 4 Bond angle restraints: 23580 Sorted by residual: angle pdb=" CA PRO D 191 " pdb=" N PRO D 191 " pdb=" CD PRO D 191 " ideal model delta sigma weight residual 112.00 104.69 7.31 1.40e+00 5.10e-01 2.73e+01 angle pdb=" N PRO D 191 " pdb=" CD PRO D 191 " pdb=" CG PRO D 191 " ideal model delta sigma weight residual 103.20 96.13 7.07 1.50e+00 4.44e-01 2.22e+01 angle pdb=" N VAL L 128 " pdb=" CA VAL L 128 " pdb=" C VAL L 128 " ideal model delta sigma weight residual 113.42 110.40 3.02 1.17e+00 7.31e-01 6.65e+00 angle pdb=" C VAL H 130 " pdb=" CA VAL H 130 " pdb=" CB VAL H 130 " ideal model delta sigma weight residual 114.35 111.63 2.72 1.06e+00 8.90e-01 6.59e+00 angle pdb=" CB PRO D 191 " pdb=" CG PRO D 191 " pdb=" CD PRO D 191 " ideal model delta sigma weight residual 106.10 97.92 8.18 3.20e+00 9.77e-02 6.53e+00 ... (remaining 23575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9312 17.97 - 35.95: 1113 35.95 - 53.92: 312 53.92 - 71.90: 85 71.90 - 89.87: 50 Dihedral angle restraints: 10872 sinusoidal: 4272 harmonic: 6600 Sorted by residual: dihedral pdb=" CB GLU J 147 " pdb=" CG GLU J 147 " pdb=" CD GLU J 147 " pdb=" OE1 GLU J 147 " ideal model delta sinusoidal sigma weight residual 0.00 89.87 -89.87 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU D 147 " pdb=" CG GLU D 147 " pdb=" CD GLU D 147 " pdb=" OE1 GLU D 147 " ideal model delta sinusoidal sigma weight residual 0.00 88.56 -88.56 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU L 147 " pdb=" CG GLU L 147 " pdb=" CD GLU L 147 " pdb=" OE1 GLU L 147 " ideal model delta sinusoidal sigma weight residual 0.00 -88.08 88.08 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 10869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2044 0.030 - 0.060: 658 0.060 - 0.089: 125 0.089 - 0.119: 87 0.119 - 0.149: 26 Chirality restraints: 2940 Sorted by residual: chirality pdb=" CA PRO E 191 " pdb=" N PRO E 191 " pdb=" C PRO E 191 " pdb=" CB PRO E 191 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" CA ILE F 124 " pdb=" N ILE F 124 " pdb=" C ILE F 124 " pdb=" CB ILE F 124 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA ILE H 124 " pdb=" N ILE H 124 " pdb=" C ILE H 124 " pdb=" CB ILE H 124 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 2937 not shown) Planarity restraints: 3144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 190 " 0.051 5.00e-02 4.00e+02 7.40e-02 8.77e+00 pdb=" N PRO D 191 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO D 191 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 191 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 21 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" C ALA C 21 " -0.034 2.00e-02 2.50e+03 pdb=" O ALA C 21 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG C 22 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP F 190 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO F 191 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO F 191 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 191 " 0.025 5.00e-02 4.00e+02 ... (remaining 3141 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 203 2.63 - 3.20: 15399 3.20 - 3.76: 28843 3.76 - 4.33: 35561 4.33 - 4.90: 61871 Nonbonded interactions: 141877 Sorted by model distance: nonbonded pdb=" OD2 ASP K 27 " pdb="ZN ZN I 201 " model vdw 2.061 2.230 nonbonded pdb=" OD2 ASP J 27 " pdb="ZN ZN J 203 " model vdw 2.061 2.230 nonbonded pdb=" OD2 ASP B 27 " pdb="ZN ZN B 201 " model vdw 2.062 2.230 nonbonded pdb=" OD2 ASP F 27 " pdb="ZN ZN H 202 " model vdw 2.066 2.230 nonbonded pdb=" OD1 ASP A 9 " pdb="ZN ZN H 201 " model vdw 2.074 2.230 ... (remaining 141872 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 6 through 193) selection = (chain 'B' and resid 6 through 193) selection = (chain 'C' and resid 6 through 193) selection = (chain 'D' and resid 6 through 193) selection = (chain 'E' and resid 6 through 193) selection = (chain 'F' and resid 6 through 193) selection = (chain 'G' and resid 6 through 193) selection = (chain 'H' and resid 6 through 193) selection = (chain 'I' and resid 6 through 193) selection = (chain 'J' and resid 6 through 193) selection = chain 'K' selection = (chain 'L' and resid 6 through 193) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.660 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 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 : 0.016 0.682 17311 Z= 0.556 Angle : 0.550 8.179 23580 Z= 0.336 Chirality : 0.035 0.149 2940 Planarity : 0.005 0.074 3144 Dihedral : 18.441 89.874 6528 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.48 % Allowed : 19.31 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.89 (0.16), residues: 2232 helix: 2.89 (0.10), residues: 1920 sheet: None (None), residues: 0 loop : 0.33 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 36 TYR 0.014 0.004 TYR J 129 PHE 0.006 0.001 PHE H 42 HIS 0.007 0.001 HIS K 23 Details of bonding type rmsd covalent geometry : bond 0.00295 (17268) covalent geometry : angle 0.54978 (23580) hydrogen bonds : bond 0.14201 ( 1538) hydrogen bonds : angle 4.15889 ( 4614) metal coordination : bond 0.32142 ( 43) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 145 time to evaluate : 0.550 Fit side-chains REVERT: B 60 GLU cc_start: 0.7950 (tp30) cc_final: 0.7567 (mm-30) REVERT: E 135 LYS cc_start: 0.8775 (ttpp) cc_final: 0.8509 (ttpp) REVERT: E 192 ASP cc_start: 0.6593 (m-30) cc_final: 0.6307 (p0) REVERT: I 187 MET cc_start: 0.8844 (mtm) cc_final: 0.8411 (mtp) REVERT: J 187 MET cc_start: 0.8452 (mtp) cc_final: 0.8213 (mtp) outliers start: 44 outliers final: 40 residues processed: 186 average time/residue: 0.6289 time to fit residues: 128.7929 Evaluate side-chains 175 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 80 SER Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 114 GLU Chi-restraints excluded: chain L residue 188 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN L 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.161473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.114397 restraints weight = 16557.354| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.42 r_work: 0.3014 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17311 Z= 0.137 Angle : 0.481 5.072 23580 Z= 0.247 Chirality : 0.035 0.145 2940 Planarity : 0.005 0.037 3144 Dihedral : 6.610 58.408 2542 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.42 % Allowed : 18.81 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.14 (0.16), residues: 2232 helix: 2.97 (0.10), residues: 1956 sheet: None (None), residues: 0 loop : 0.79 (0.45), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 36 TYR 0.015 0.004 TYR I 129 PHE 0.006 0.001 PHE H 42 HIS 0.005 0.001 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00283 (17268) covalent geometry : angle 0.48129 (23580) hydrogen bonds : bond 0.05786 ( 1538) hydrogen bonds : angle 3.51548 ( 4614) metal coordination : bond 0.00570 ( 43) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 146 time to evaluate : 0.515 Fit side-chains REVERT: B 60 GLU cc_start: 0.8329 (tp30) cc_final: 0.7975 (mm-30) REVERT: D 55 VAL cc_start: 0.8057 (t) cc_final: 0.7839 (p) REVERT: E 30 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8353 (mp) REVERT: E 192 ASP cc_start: 0.6559 (m-30) cc_final: 0.6011 (p0) REVERT: J 187 MET cc_start: 0.8318 (mtp) cc_final: 0.7932 (mtp) outliers start: 43 outliers final: 28 residues processed: 185 average time/residue: 0.6247 time to fit residues: 127.5360 Evaluate side-chains 165 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 128 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 198 optimal weight: 20.0000 chunk 3 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.162678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.114973 restraints weight = 16685.669| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.50 r_work: 0.3030 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17311 Z= 0.122 Angle : 0.453 4.841 23580 Z= 0.232 Chirality : 0.035 0.144 2940 Planarity : 0.005 0.037 3144 Dihedral : 5.967 59.929 2517 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.48 % Allowed : 18.41 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.47 (0.17), residues: 2232 helix: 3.15 (0.10), residues: 1956 sheet: None (None), residues: 0 loop : 1.31 (0.49), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 120 TYR 0.015 0.004 TYR I 129 PHE 0.007 0.001 PHE F 42 HIS 0.005 0.001 HIS B 23 Details of bonding type rmsd covalent geometry : bond 0.00243 (17268) covalent geometry : angle 0.45336 (23580) hydrogen bonds : bond 0.05223 ( 1538) hydrogen bonds : angle 3.33634 ( 4614) metal coordination : bond 0.00230 ( 43) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 137 time to evaluate : 0.497 Fit side-chains REVERT: B 23 HIS cc_start: 0.8127 (t-170) cc_final: 0.7850 (t-170) REVERT: B 60 GLU cc_start: 0.8322 (tp30) cc_final: 0.7997 (mm-30) REVERT: E 30 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8299 (mp) REVERT: E 192 ASP cc_start: 0.6615 (m-30) cc_final: 0.6046 (p0) REVERT: G 190 ASP cc_start: 0.6425 (t70) cc_final: 0.6223 (t0) REVERT: J 187 MET cc_start: 0.8252 (mtp) cc_final: 0.7798 (mtp) REVERT: K 40 GLU cc_start: 0.7996 (pp20) cc_final: 0.7750 (pp20) REVERT: L 186 ARG cc_start: 0.8351 (mtp-110) cc_final: 0.8084 (mtm110) outliers start: 44 outliers final: 30 residues processed: 176 average time/residue: 0.5960 time to fit residues: 115.7739 Evaluate side-chains 161 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 128 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 154 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 206 optimal weight: 7.9990 chunk 192 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 213 optimal weight: 0.7980 chunk 214 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 212 optimal weight: 0.9990 chunk 181 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.160792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.114304 restraints weight = 16751.959| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.50 r_work: 0.2984 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17311 Z= 0.145 Angle : 0.468 4.923 23580 Z= 0.237 Chirality : 0.035 0.139 2940 Planarity : 0.005 0.038 3144 Dihedral : 5.687 58.742 2511 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.04 % Allowed : 18.24 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.46 (0.17), residues: 2232 helix: 3.12 (0.10), residues: 1956 sheet: None (None), residues: 0 loop : 1.50 (0.50), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 36 TYR 0.017 0.004 TYR I 129 PHE 0.006 0.001 PHE J 42 HIS 0.003 0.001 HIS B 23 Details of bonding type rmsd covalent geometry : bond 0.00329 (17268) covalent geometry : angle 0.46829 (23580) hydrogen bonds : bond 0.05634 ( 1538) hydrogen bonds : angle 3.36078 ( 4614) metal coordination : bond 0.00265 ( 43) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 143 time to evaluate : 0.557 Fit side-chains REVERT: B 23 HIS cc_start: 0.8396 (t-170) cc_final: 0.8107 (t-170) REVERT: B 60 GLU cc_start: 0.8382 (tp30) cc_final: 0.8054 (mm-30) REVERT: C 30 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8521 (mp) REVERT: E 30 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8358 (mp) REVERT: E 192 ASP cc_start: 0.6584 (m-30) cc_final: 0.6015 (p0) REVERT: G 190 ASP cc_start: 0.6494 (t70) cc_final: 0.6236 (OUTLIER) REVERT: J 187 MET cc_start: 0.8412 (mtp) cc_final: 0.7942 (mtp) REVERT: L 186 ARG cc_start: 0.8384 (mtp-110) cc_final: 0.8086 (mtm110) outliers start: 54 outliers final: 38 residues processed: 190 average time/residue: 0.6274 time to fit residues: 130.9947 Evaluate side-chains 174 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 186 ARG Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 128 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 214 optimal weight: 0.0020 chunk 183 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 165 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 31 optimal weight: 0.0770 chunk 194 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 overall best weight: 0.8152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.163122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.115401 restraints weight = 16577.188| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.50 r_work: 0.3025 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17311 Z= 0.116 Angle : 0.441 4.824 23580 Z= 0.224 Chirality : 0.034 0.141 2940 Planarity : 0.005 0.036 3144 Dihedral : 5.524 58.839 2511 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.59 % Allowed : 18.64 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.75 (0.17), residues: 2232 helix: 3.33 (0.10), residues: 1956 sheet: None (None), residues: 0 loop : 1.47 (0.49), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 36 TYR 0.015 0.004 TYR I 129 PHE 0.007 0.001 PHE J 42 HIS 0.003 0.001 HIS H 23 Details of bonding type rmsd covalent geometry : bond 0.00227 (17268) covalent geometry : angle 0.44057 (23580) hydrogen bonds : bond 0.04983 ( 1538) hydrogen bonds : angle 3.24952 ( 4614) metal coordination : bond 0.00154 ( 43) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 140 time to evaluate : 0.621 Fit side-chains REVERT: B 23 HIS cc_start: 0.8274 (t-170) cc_final: 0.7994 (t-170) REVERT: B 60 GLU cc_start: 0.8331 (tp30) cc_final: 0.8006 (mm-30) REVERT: C 30 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8608 (mp) REVERT: E 30 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8250 (mp) REVERT: E 192 ASP cc_start: 0.6591 (m-30) cc_final: 0.6013 (p0) REVERT: J 36 ARG cc_start: 0.7675 (ttp80) cc_final: 0.7287 (ttp80) REVERT: J 90 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8498 (mp) REVERT: J 187 MET cc_start: 0.8183 (mtp) cc_final: 0.7881 (mtp) outliers start: 46 outliers final: 32 residues processed: 179 average time/residue: 0.5947 time to fit residues: 117.1998 Evaluate side-chains 165 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 186 ARG Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 0.9980 chunk 185 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 172 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 195 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 123 ASN L 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.160205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.113334 restraints weight = 16585.122| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.31 r_work: 0.3003 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17311 Z= 0.160 Angle : 0.481 4.952 23580 Z= 0.243 Chirality : 0.036 0.139 2940 Planarity : 0.005 0.039 3144 Dihedral : 5.570 59.764 2510 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.93 % Allowed : 18.69 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.55 (0.17), residues: 2232 helix: 3.17 (0.10), residues: 1956 sheet: None (None), residues: 0 loop : 1.60 (0.49), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 36 TYR 0.017 0.005 TYR I 129 PHE 0.006 0.001 PHE F 42 HIS 0.003 0.001 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00376 (17268) covalent geometry : angle 0.48059 (23580) hydrogen bonds : bond 0.05819 ( 1538) hydrogen bonds : angle 3.34228 ( 4614) metal coordination : bond 0.00277 ( 43) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 135 time to evaluate : 0.593 Fit side-chains REVERT: B 23 HIS cc_start: 0.8421 (t-170) cc_final: 0.8139 (t-170) REVERT: B 60 GLU cc_start: 0.8452 (tp30) cc_final: 0.8124 (mm-30) REVERT: C 30 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8674 (mm) REVERT: E 16 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7513 (tt0) REVERT: E 30 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8390 (mp) REVERT: E 192 ASP cc_start: 0.6627 (m-30) cc_final: 0.6096 (p0) REVERT: J 36 ARG cc_start: 0.7734 (ttp80) cc_final: 0.7400 (ttp80) REVERT: J 187 MET cc_start: 0.8487 (mtp) cc_final: 0.8013 (mtp) REVERT: K 40 GLU cc_start: 0.7992 (pp20) cc_final: 0.7781 (pp20) outliers start: 52 outliers final: 37 residues processed: 179 average time/residue: 0.6125 time to fit residues: 120.3602 Evaluate side-chains 173 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 16 GLU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 186 ARG Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 126 SER Chi-restraints excluded: chain L residue 128 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 163 optimal weight: 6.9990 chunk 213 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 79 optimal weight: 0.0170 chunk 204 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 overall best weight: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN D 15 GLN I 15 GLN J 123 ASN L 15 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.163459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.115676 restraints weight = 16507.906| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.49 r_work: 0.3045 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17311 Z= 0.114 Angle : 0.438 4.787 23580 Z= 0.224 Chirality : 0.034 0.145 2940 Planarity : 0.004 0.035 3144 Dihedral : 5.249 59.181 2508 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.48 % Allowed : 18.92 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.87 (0.17), residues: 2232 helix: 3.41 (0.10), residues: 1956 sheet: None (None), residues: 0 loop : 1.46 (0.47), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 120 TYR 0.015 0.004 TYR I 129 PHE 0.007 0.001 PHE J 42 HIS 0.003 0.001 HIS H 23 Details of bonding type rmsd covalent geometry : bond 0.00221 (17268) covalent geometry : angle 0.43850 (23580) hydrogen bonds : bond 0.04875 ( 1538) hydrogen bonds : angle 3.19772 ( 4614) metal coordination : bond 0.00154 ( 43) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 136 time to evaluate : 0.677 Fit side-chains REVERT: B 23 HIS cc_start: 0.8319 (t-170) cc_final: 0.8069 (t-170) REVERT: B 60 GLU cc_start: 0.8350 (tp30) cc_final: 0.8013 (mm-30) REVERT: E 30 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8324 (mp) REVERT: E 192 ASP cc_start: 0.6590 (m-30) cc_final: 0.6032 (p0) REVERT: G 30 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8241 (tp) REVERT: J 36 ARG cc_start: 0.7715 (ttp80) cc_final: 0.7337 (ttp80) REVERT: J 90 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8542 (mp) REVERT: K 40 GLU cc_start: 0.7905 (pp20) cc_final: 0.7666 (pp20) outliers start: 44 outliers final: 30 residues processed: 171 average time/residue: 0.6657 time to fit residues: 125.2399 Evaluate side-chains 166 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 128 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 211 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 133 optimal weight: 0.6980 chunk 112 optimal weight: 20.0000 chunk 113 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.163472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.115683 restraints weight = 16721.331| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.49 r_work: 0.3043 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 17311 Z= 0.116 Angle : 0.444 4.833 23580 Z= 0.226 Chirality : 0.034 0.142 2940 Planarity : 0.004 0.036 3144 Dihedral : 4.916 57.666 2504 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.14 % Allowed : 19.37 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.93 (0.17), residues: 2232 helix: 3.45 (0.10), residues: 1956 sheet: None (None), residues: 0 loop : 1.51 (0.47), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 36 TYR 0.016 0.004 TYR I 129 PHE 0.006 0.001 PHE F 42 HIS 0.003 0.001 HIS H 23 Details of bonding type rmsd covalent geometry : bond 0.00232 (17268) covalent geometry : angle 0.44397 (23580) hydrogen bonds : bond 0.04870 ( 1538) hydrogen bonds : angle 3.18759 ( 4614) metal coordination : bond 0.00187 ( 43) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 0.626 Fit side-chains REVERT: B 23 HIS cc_start: 0.8292 (t-170) cc_final: 0.8003 (t-170) REVERT: B 60 GLU cc_start: 0.8429 (tp30) cc_final: 0.8104 (mm-30) REVERT: E 40 GLU cc_start: 0.8003 (pp20) cc_final: 0.7794 (pp20) REVERT: E 192 ASP cc_start: 0.6603 (m-30) cc_final: 0.6024 (p0) REVERT: G 30 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8274 (tp) REVERT: J 36 ARG cc_start: 0.7776 (ttp80) cc_final: 0.7336 (ttp80) REVERT: J 90 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8542 (mp) REVERT: J 118 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8677 (tp) REVERT: K 40 GLU cc_start: 0.7972 (pp20) cc_final: 0.7758 (pp20) outliers start: 38 outliers final: 28 residues processed: 175 average time/residue: 0.6766 time to fit residues: 130.4946 Evaluate side-chains 168 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 115 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 187 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 15 GLN L 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.162941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.115110 restraints weight = 16584.356| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.48 r_work: 0.3035 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17311 Z= 0.123 Angle : 0.456 6.222 23580 Z= 0.232 Chirality : 0.035 0.141 2940 Planarity : 0.004 0.037 3144 Dihedral : 4.882 56.576 2504 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.08 % Allowed : 19.71 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.90 (0.17), residues: 2232 helix: 3.42 (0.10), residues: 1956 sheet: None (None), residues: 0 loop : 1.55 (0.47), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 36 TYR 0.016 0.004 TYR I 129 PHE 0.006 0.001 PHE E 42 HIS 0.003 0.001 HIS H 23 Details of bonding type rmsd covalent geometry : bond 0.00260 (17268) covalent geometry : angle 0.45622 (23580) hydrogen bonds : bond 0.05021 ( 1538) hydrogen bonds : angle 3.18835 ( 4614) metal coordination : bond 0.00163 ( 43) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.794 Fit side-chains REVERT: B 23 HIS cc_start: 0.8311 (t-170) cc_final: 0.8048 (t-170) REVERT: B 60 GLU cc_start: 0.8437 (tp30) cc_final: 0.8110 (mm-30) REVERT: E 192 ASP cc_start: 0.6595 (m-30) cc_final: 0.6030 (p0) REVERT: G 30 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8298 (tp) REVERT: I 40 GLU cc_start: 0.7990 (pp20) cc_final: 0.7652 (pp20) REVERT: J 36 ARG cc_start: 0.7690 (ttp80) cc_final: 0.7312 (ttp80) REVERT: J 90 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8542 (mp) outliers start: 37 outliers final: 28 residues processed: 173 average time/residue: 0.7100 time to fit residues: 134.9421 Evaluate side-chains 168 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 92 optimal weight: 0.3980 chunk 62 optimal weight: 7.9990 chunk 205 optimal weight: 0.6980 chunk 191 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 66 optimal weight: 0.0470 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 15 GLN L 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.163922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.116378 restraints weight = 16515.945| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.48 r_work: 0.3051 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17311 Z= 0.115 Angle : 0.460 8.597 23580 Z= 0.236 Chirality : 0.035 0.142 2940 Planarity : 0.004 0.036 3144 Dihedral : 4.604 54.881 2501 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.91 % Allowed : 19.99 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.99 (0.17), residues: 2232 helix: 3.48 (0.10), residues: 1956 sheet: None (None), residues: 0 loop : 1.56 (0.47), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 36 TYR 0.015 0.004 TYR I 129 PHE 0.007 0.001 PHE L 42 HIS 0.003 0.001 HIS H 23 Details of bonding type rmsd covalent geometry : bond 0.00230 (17268) covalent geometry : angle 0.46036 (23580) hydrogen bonds : bond 0.04785 ( 1538) hydrogen bonds : angle 3.15554 ( 4614) metal coordination : bond 0.00122 ( 43) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.710 Fit side-chains REVERT: B 23 HIS cc_start: 0.8279 (t-170) cc_final: 0.8017 (t-170) REVERT: B 60 GLU cc_start: 0.8429 (tp30) cc_final: 0.8101 (mm-30) REVERT: E 20 LYS cc_start: 0.8126 (tptt) cc_final: 0.7813 (mmmt) REVERT: E 192 ASP cc_start: 0.6582 (m-30) cc_final: 0.6001 (p0) REVERT: G 30 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8294 (tp) REVERT: I 40 GLU cc_start: 0.8010 (pp20) cc_final: 0.7682 (pp20) REVERT: I 60 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8214 (mm-30) REVERT: J 36 ARG cc_start: 0.7690 (ttp80) cc_final: 0.7342 (ttp80) REVERT: J 90 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8535 (mp) outliers start: 34 outliers final: 27 residues processed: 174 average time/residue: 0.7208 time to fit residues: 137.3499 Evaluate side-chains 173 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 42 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 114 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 66 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 186 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.164088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.116505 restraints weight = 16541.111| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.52 r_work: 0.3051 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17311 Z= 0.116 Angle : 0.463 7.943 23580 Z= 0.237 Chirality : 0.035 0.141 2940 Planarity : 0.004 0.036 3144 Dihedral : 4.440 55.513 2499 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.97 % Allowed : 19.76 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.00 (0.17), residues: 2232 helix: 3.49 (0.10), residues: 1956 sheet: None (None), residues: 0 loop : 1.60 (0.46), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 36 TYR 0.015 0.004 TYR I 129 PHE 0.008 0.001 PHE B 42 HIS 0.003 0.001 HIS H 23 Details of bonding type rmsd covalent geometry : bond 0.00235 (17268) covalent geometry : angle 0.46298 (23580) hydrogen bonds : bond 0.04766 ( 1538) hydrogen bonds : angle 3.13972 ( 4614) metal coordination : bond 0.00115 ( 43) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5150.92 seconds wall clock time: 88 minutes 11.03 seconds (5291.03 seconds total)