Starting phenix.real_space_refine on Mon Sep 30 10:47:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pv2_13664/09_2024/7pv2_13664.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pv2_13664/09_2024/7pv2_13664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pv2_13664/09_2024/7pv2_13664.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pv2_13664/09_2024/7pv2_13664.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pv2_13664/09_2024/7pv2_13664.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pv2_13664/09_2024/7pv2_13664.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 16476 2.51 5 N 4176 2.21 5 O 4680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 25440 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "B" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "C" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "D" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "E" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "F" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "G" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "H" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "I" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "J" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "K" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "L" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Time building chain proxies: 13.46, per 1000 atoms: 0.53 Number of scatterers: 25440 At special positions: 0 Unit cell: (167.99, 167.99, 88.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 4680 8.00 N 4176 7.00 C 16476 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: 6.12 Conformation dependent library (CDL) restraints added in 2.9 seconds 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5760 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 48 sheets defined 42.4% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'A' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE A 14 " --> pdb=" O THR A 10 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 16 " --> pdb=" O GLY A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 36 removed outlier: 3.848A pdb=" N ARG A 24 " --> pdb=" O ASN A 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 60 Processing helix chain 'A' and resid 132 through 155 removed outlier: 3.726A pdb=" N LEU A 136 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 177 removed outlier: 3.725A pdb=" N MET A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR A 177 " --> pdb=" O MET A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 228 removed outlier: 3.675A pdb=" N PHE A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 274 Proline residue: A 262 - end of helix Processing helix chain 'B' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE B 14 " --> pdb=" O THR B 10 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 36 removed outlier: 3.848A pdb=" N ARG B 24 " --> pdb=" O ASN B 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 60 Processing helix chain 'B' and resid 132 through 155 removed outlier: 3.726A pdb=" N LEU B 136 " --> pdb=" O THR B 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET B 141 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 removed outlier: 3.724A pdb=" N MET B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR B 177 " --> pdb=" O MET B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 228 removed outlier: 3.676A pdb=" N PHE B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 274 Proline residue: B 262 - end of helix Processing helix chain 'C' and resid 10 through 16 removed outlier: 3.630A pdb=" N ILE C 14 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 36 removed outlier: 3.849A pdb=" N ARG C 24 " --> pdb=" O ASN C 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER C 32 " --> pdb=" O ARG C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 60 Processing helix chain 'C' and resid 132 through 155 removed outlier: 3.727A pdb=" N LEU C 136 " --> pdb=" O THR C 132 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU C 138 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET C 141 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR C 151 " --> pdb=" O LYS C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 177 removed outlier: 3.725A pdb=" N MET C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL C 176 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR C 177 " --> pdb=" O MET C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 228 removed outlier: 3.677A pdb=" N PHE C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 274 Proline residue: C 262 - end of helix Processing helix chain 'D' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE D 14 " --> pdb=" O THR D 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG D 16 " --> pdb=" O GLY D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 36 removed outlier: 3.848A pdb=" N ARG D 24 " --> pdb=" O ASN D 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 60 Processing helix chain 'D' and resid 132 through 155 removed outlier: 3.726A pdb=" N LEU D 136 " --> pdb=" O THR D 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR D 151 " --> pdb=" O LYS D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 177 removed outlier: 3.724A pdb=" N MET D 173 " --> pdb=" O ASP D 169 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR D 177 " --> pdb=" O MET D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 228 removed outlier: 3.676A pdb=" N PHE D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 274 Proline residue: D 262 - end of helix Processing helix chain 'E' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE E 14 " --> pdb=" O THR E 10 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG E 16 " --> pdb=" O GLY E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 36 removed outlier: 3.849A pdb=" N ARG E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 60 Processing helix chain 'E' and resid 132 through 155 removed outlier: 3.726A pdb=" N LEU E 136 " --> pdb=" O THR E 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU E 138 " --> pdb=" O ASP E 134 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET E 141 " --> pdb=" O ASN E 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR E 151 " --> pdb=" O LYS E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 177 removed outlier: 3.725A pdb=" N MET E 173 " --> pdb=" O ASP E 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL E 176 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR E 177 " --> pdb=" O MET E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 228 removed outlier: 3.676A pdb=" N PHE E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 274 Proline residue: E 262 - end of helix Processing helix chain 'F' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE F 14 " --> pdb=" O THR F 10 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG F 16 " --> pdb=" O GLY F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 36 removed outlier: 3.849A pdb=" N ARG F 24 " --> pdb=" O ASN F 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER F 32 " --> pdb=" O ARG F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 60 Processing helix chain 'F' and resid 132 through 155 removed outlier: 3.726A pdb=" N LEU F 136 " --> pdb=" O THR F 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET F 141 " --> pdb=" O ASN F 137 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR F 151 " --> pdb=" O LYS F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 177 removed outlier: 3.725A pdb=" N MET F 173 " --> pdb=" O ASP F 169 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL F 176 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR F 177 " --> pdb=" O MET F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 228 removed outlier: 3.676A pdb=" N PHE F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 274 Proline residue: F 262 - end of helix Processing helix chain 'G' and resid 10 through 16 removed outlier: 3.632A pdb=" N ILE G 14 " --> pdb=" O THR G 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG G 16 " --> pdb=" O GLY G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 36 removed outlier: 3.848A pdb=" N ARG G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER G 32 " --> pdb=" O ARG G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 60 Processing helix chain 'G' and resid 132 through 155 removed outlier: 3.726A pdb=" N LEU G 136 " --> pdb=" O THR G 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU G 138 " --> pdb=" O ASP G 134 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET G 141 " --> pdb=" O ASN G 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR G 151 " --> pdb=" O LYS G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 177 removed outlier: 3.724A pdb=" N MET G 173 " --> pdb=" O ASP G 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL G 176 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TYR G 177 " --> pdb=" O MET G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 228 removed outlier: 3.676A pdb=" N PHE G 216 " --> pdb=" O LEU G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 274 Proline residue: G 262 - end of helix Processing helix chain 'H' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE H 14 " --> pdb=" O THR H 10 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG H 16 " --> pdb=" O GLY H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 36 removed outlier: 3.848A pdb=" N ARG H 24 " --> pdb=" O ASN H 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER H 32 " --> pdb=" O ARG H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 60 Processing helix chain 'H' and resid 132 through 155 removed outlier: 3.726A pdb=" N LEU H 136 " --> pdb=" O THR H 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU H 138 " --> pdb=" O ASP H 134 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET H 141 " --> pdb=" O ASN H 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR H 151 " --> pdb=" O LYS H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 177 removed outlier: 3.724A pdb=" N MET H 173 " --> pdb=" O ASP H 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL H 176 " --> pdb=" O SER H 172 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR H 177 " --> pdb=" O MET H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 228 removed outlier: 3.676A pdb=" N PHE H 216 " --> pdb=" O LEU H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 274 Proline residue: H 262 - end of helix Processing helix chain 'I' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE I 14 " --> pdb=" O THR I 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG I 16 " --> pdb=" O GLY I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 36 removed outlier: 3.848A pdb=" N ARG I 24 " --> pdb=" O ASN I 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER I 32 " --> pdb=" O ARG I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 60 Processing helix chain 'I' and resid 132 through 155 removed outlier: 3.727A pdb=" N LEU I 136 " --> pdb=" O THR I 132 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU I 138 " --> pdb=" O ASP I 134 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET I 141 " --> pdb=" O ASN I 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR I 151 " --> pdb=" O LYS I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 177 removed outlier: 3.725A pdb=" N MET I 173 " --> pdb=" O ASP I 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL I 176 " --> pdb=" O SER I 172 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TYR I 177 " --> pdb=" O MET I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 228 removed outlier: 3.677A pdb=" N PHE I 216 " --> pdb=" O LEU I 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 256 through 274 Proline residue: I 262 - end of helix Processing helix chain 'J' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE J 14 " --> pdb=" O THR J 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG J 16 " --> pdb=" O GLY J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 36 removed outlier: 3.847A pdb=" N ARG J 24 " --> pdb=" O ASN J 20 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER J 32 " --> pdb=" O ARG J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 60 Processing helix chain 'J' and resid 132 through 155 removed outlier: 3.727A pdb=" N LEU J 136 " --> pdb=" O THR J 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU J 138 " --> pdb=" O ASP J 134 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET J 141 " --> pdb=" O ASN J 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR J 151 " --> pdb=" O LYS J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 169 through 177 removed outlier: 3.725A pdb=" N MET J 173 " --> pdb=" O ASP J 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL J 176 " --> pdb=" O SER J 172 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR J 177 " --> pdb=" O MET J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 228 removed outlier: 3.675A pdb=" N PHE J 216 " --> pdb=" O LEU J 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 274 Proline residue: J 262 - end of helix Processing helix chain 'K' and resid 10 through 16 removed outlier: 3.632A pdb=" N ILE K 14 " --> pdb=" O THR K 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 36 removed outlier: 3.848A pdb=" N ARG K 24 " --> pdb=" O ASN K 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER K 32 " --> pdb=" O ARG K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 60 Processing helix chain 'K' and resid 132 through 155 removed outlier: 3.726A pdb=" N LEU K 136 " --> pdb=" O THR K 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU K 138 " --> pdb=" O ASP K 134 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET K 141 " --> pdb=" O ASN K 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR K 151 " --> pdb=" O LYS K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 169 through 177 removed outlier: 3.724A pdb=" N MET K 173 " --> pdb=" O ASP K 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL K 176 " --> pdb=" O SER K 172 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR K 177 " --> pdb=" O MET K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 228 removed outlier: 3.676A pdb=" N PHE K 216 " --> pdb=" O LEU K 212 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 274 Proline residue: K 262 - end of helix Processing helix chain 'L' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE L 14 " --> pdb=" O THR L 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG L 16 " --> pdb=" O GLY L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 36 removed outlier: 3.848A pdb=" N ARG L 24 " --> pdb=" O ASN L 20 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER L 32 " --> pdb=" O ARG L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 60 Processing helix chain 'L' and resid 132 through 155 removed outlier: 3.727A pdb=" N LEU L 136 " --> pdb=" O THR L 132 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU L 138 " --> pdb=" O ASP L 134 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET L 141 " --> pdb=" O ASN L 137 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR L 151 " --> pdb=" O LYS L 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 169 through 177 removed outlier: 3.725A pdb=" N MET L 173 " --> pdb=" O ASP L 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL L 176 " --> pdb=" O SER L 172 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR L 177 " --> pdb=" O MET L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 228 removed outlier: 3.676A pdb=" N PHE L 216 " --> pdb=" O LEU L 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 256 through 274 Proline residue: L 262 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 41 removed outlier: 3.503A pdb=" N LYS A 281 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 279 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AA4, first strand: chain 'A' and resid 199 through 202 removed outlier: 7.171A pdb=" N VAL A 161 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N PHE B 188 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 163 " --> pdb=" O PHE B 188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 189 removed outlier: 4.150A pdb=" N VAL A 186 " --> pdb=" O VAL L 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 38 through 41 removed outlier: 3.502A pdb=" N LYS B 281 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 279 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 74 through 75 Processing sheet with id=AA8, first strand: chain 'B' and resid 91 through 93 Processing sheet with id=AA9, first strand: chain 'B' and resid 199 through 202 removed outlier: 7.171A pdb=" N VAL B 161 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N PHE C 188 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 163 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 38 through 41 removed outlier: 3.503A pdb=" N LYS C 281 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER C 279 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 74 through 75 Processing sheet with id=AB3, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AB4, first strand: chain 'C' and resid 199 through 202 removed outlier: 7.170A pdb=" N VAL C 161 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N PHE D 188 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE C 163 " --> pdb=" O PHE D 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 38 through 41 removed outlier: 3.502A pdb=" N LYS D 281 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER D 279 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 74 through 75 Processing sheet with id=AB7, first strand: chain 'D' and resid 91 through 93 Processing sheet with id=AB8, first strand: chain 'D' and resid 199 through 202 removed outlier: 7.171A pdb=" N VAL D 161 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N PHE E 188 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE D 163 " --> pdb=" O PHE E 188 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 38 through 41 removed outlier: 3.502A pdb=" N LYS E 281 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER E 279 " --> pdb=" O GLN E 41 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 74 through 75 Processing sheet with id=AC2, first strand: chain 'E' and resid 91 through 93 Processing sheet with id=AC3, first strand: chain 'E' and resid 199 through 202 removed outlier: 7.171A pdb=" N VAL E 161 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N PHE F 188 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE E 163 " --> pdb=" O PHE F 188 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 38 through 41 removed outlier: 3.503A pdb=" N LYS F 281 " --> pdb=" O GLU F 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER F 279 " --> pdb=" O GLN F 41 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 74 through 75 Processing sheet with id=AC6, first strand: chain 'F' and resid 91 through 93 Processing sheet with id=AC7, first strand: chain 'F' and resid 199 through 202 removed outlier: 7.248A pdb=" N VAL F 161 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N PHE G 188 " --> pdb=" O VAL F 161 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE F 163 " --> pdb=" O PHE G 188 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 38 through 41 removed outlier: 3.503A pdb=" N LYS G 281 " --> pdb=" O GLU G 39 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER G 279 " --> pdb=" O GLN G 41 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 74 through 75 Processing sheet with id=AD1, first strand: chain 'G' and resid 91 through 93 Processing sheet with id=AD2, first strand: chain 'G' and resid 199 through 202 removed outlier: 4.220A pdb=" N VAL H 186 " --> pdb=" O VAL G 161 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 38 through 41 removed outlier: 3.503A pdb=" N LYS H 281 " --> pdb=" O GLU H 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER H 279 " --> pdb=" O GLN H 41 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 74 through 75 Processing sheet with id=AD5, first strand: chain 'H' and resid 91 through 93 Processing sheet with id=AD6, first strand: chain 'H' and resid 199 through 202 removed outlier: 7.171A pdb=" N VAL H 161 " --> pdb=" O VAL I 186 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N PHE I 188 " --> pdb=" O VAL H 161 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE H 163 " --> pdb=" O PHE I 188 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 38 through 41 removed outlier: 3.502A pdb=" N LYS I 281 " --> pdb=" O GLU I 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER I 279 " --> pdb=" O GLN I 41 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 74 through 75 Processing sheet with id=AD9, first strand: chain 'I' and resid 91 through 93 Processing sheet with id=AE1, first strand: chain 'I' and resid 199 through 202 removed outlier: 7.171A pdb=" N VAL I 161 " --> pdb=" O VAL J 186 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N PHE J 188 " --> pdb=" O VAL I 161 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE I 163 " --> pdb=" O PHE J 188 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 38 through 41 removed outlier: 3.503A pdb=" N LYS J 281 " --> pdb=" O GLU J 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER J 279 " --> pdb=" O GLN J 41 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 74 through 75 Processing sheet with id=AE4, first strand: chain 'J' and resid 91 through 93 Processing sheet with id=AE5, first strand: chain 'J' and resid 199 through 202 removed outlier: 7.172A pdb=" N VAL J 161 " --> pdb=" O VAL K 186 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N PHE K 188 " --> pdb=" O VAL J 161 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE J 163 " --> pdb=" O PHE K 188 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 38 through 41 removed outlier: 3.502A pdb=" N LYS K 281 " --> pdb=" O GLU K 39 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER K 279 " --> pdb=" O GLN K 41 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 74 through 75 Processing sheet with id=AE8, first strand: chain 'K' and resid 91 through 93 Processing sheet with id=AE9, first strand: chain 'K' and resid 199 through 202 removed outlier: 7.171A pdb=" N VAL K 161 " --> pdb=" O VAL L 186 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N PHE L 188 " --> pdb=" O VAL K 161 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE K 163 " --> pdb=" O PHE L 188 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 38 through 41 removed outlier: 3.502A pdb=" N LYS L 281 " --> pdb=" O GLU L 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER L 279 " --> pdb=" O GLN L 41 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 74 through 75 Processing sheet with id=AF3, first strand: chain 'L' and resid 91 through 93 966 hydrogen bonds defined for protein. 2826 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: 7.23 Time building geometry restraints manager: 7.12 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: 8053 1.34 - 1.46: 6031 1.46 - 1.57: 11764 1.57 - 1.69: 0 1.69 - 1.81: 204 Bond restraints: 26052 Sorted by residual: bond pdb=" CB ILE A 150 " pdb=" CG2 ILE A 150 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.83e+00 bond pdb=" CB ILE D 150 " pdb=" CG2 ILE D 150 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.79e+00 bond pdb=" CB ILE E 150 " pdb=" CG2 ILE E 150 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.76e+00 bond pdb=" CB ILE B 150 " pdb=" CG2 ILE B 150 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.76e+00 bond pdb=" CB ILE H 150 " pdb=" CG2 ILE H 150 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.76e+00 ... (remaining 26047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 33302 1.40 - 2.81: 1614 2.81 - 4.21: 259 4.21 - 5.62: 45 5.62 - 7.02: 12 Bond angle restraints: 35232 Sorted by residual: angle pdb=" CA GLY E 190 " pdb=" C GLY E 190 " pdb=" O GLY E 190 " ideal model delta sigma weight residual 122.37 120.45 1.92 7.30e-01 1.88e+00 6.94e+00 angle pdb=" CA GLY H 190 " pdb=" C GLY H 190 " pdb=" O GLY H 190 " ideal model delta sigma weight residual 122.37 120.45 1.92 7.30e-01 1.88e+00 6.94e+00 angle pdb=" CA GLY D 190 " pdb=" C GLY D 190 " pdb=" O GLY D 190 " ideal model delta sigma weight residual 122.37 120.47 1.90 7.30e-01 1.88e+00 6.79e+00 angle pdb=" CA GLY B 190 " pdb=" C GLY B 190 " pdb=" O GLY B 190 " ideal model delta sigma weight residual 122.37 120.47 1.90 7.30e-01 1.88e+00 6.75e+00 angle pdb=" CA GLY J 190 " pdb=" C GLY J 190 " pdb=" O GLY J 190 " ideal model delta sigma weight residual 122.37 120.48 1.89 7.30e-01 1.88e+00 6.73e+00 ... (remaining 35227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.55: 13368 15.55 - 31.09: 1692 31.09 - 46.64: 223 46.64 - 62.19: 101 62.19 - 77.74: 84 Dihedral angle restraints: 15468 sinusoidal: 6396 harmonic: 9072 Sorted by residual: dihedral pdb=" CA LEU L 73 " pdb=" C LEU L 73 " pdb=" N GLY L 74 " pdb=" CA GLY L 74 " ideal model delta harmonic sigma weight residual 180.00 163.80 16.20 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA LEU F 73 " pdb=" C LEU F 73 " pdb=" N GLY F 74 " pdb=" CA GLY F 74 " ideal model delta harmonic sigma weight residual 180.00 163.81 16.19 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA LEU I 73 " pdb=" C LEU I 73 " pdb=" N GLY I 74 " pdb=" CA GLY I 74 " ideal model delta harmonic sigma weight residual 180.00 163.83 16.17 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 15465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 3090 0.086 - 0.171: 383 0.171 - 0.257: 108 0.257 - 0.343: 79 0.343 - 0.428: 24 Chirality restraints: 3684 Sorted by residual: chirality pdb=" CB ILE A 135 " pdb=" CA ILE A 135 " pdb=" CG1 ILE A 135 " pdb=" CG2 ILE A 135 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" CB ILE K 135 " pdb=" CA ILE K 135 " pdb=" CG1 ILE K 135 " pdb=" CG2 ILE K 135 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" CB ILE E 135 " pdb=" CA ILE E 135 " pdb=" CG1 ILE E 135 " pdb=" CG2 ILE E 135 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.55e+00 ... (remaining 3681 not shown) Planarity restraints: 4536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN J 251 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" CD GLN J 251 " 0.041 2.00e-02 2.50e+03 pdb=" OE1 GLN J 251 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN J 251 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 251 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" CD GLN A 251 " 0.041 2.00e-02 2.50e+03 pdb=" OE1 GLN A 251 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN A 251 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN H 251 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" CD GLN H 251 " 0.040 2.00e-02 2.50e+03 pdb=" OE1 GLN H 251 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN H 251 " -0.014 2.00e-02 2.50e+03 ... (remaining 4533 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 205 2.56 - 3.14: 20668 3.14 - 3.73: 35405 3.73 - 4.31: 51075 4.31 - 4.90: 88641 Nonbonded interactions: 195994 Sorted by model distance: nonbonded pdb=" OD1 ASP J 169 " pdb=" OG SER J 172 " model vdw 1.971 3.040 nonbonded pdb=" OD1 ASP B 169 " pdb=" OG SER B 172 " model vdw 1.971 3.040 nonbonded pdb=" OD1 ASP K 169 " pdb=" OG SER K 172 " model vdw 1.971 3.040 nonbonded pdb=" OD1 ASP D 169 " pdb=" OG SER D 172 " model vdw 1.971 3.040 nonbonded pdb=" OD1 ASP F 169 " pdb=" OG SER F 172 " model vdw 1.971 3.040 ... (remaining 195989 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 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: 0.870 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 50.500 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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 : 0.011 0.070 26052 Z= 0.695 Angle : 0.714 7.019 35232 Z= 0.392 Chirality : 0.084 0.428 3684 Planarity : 0.004 0.039 4536 Dihedral : 14.851 77.735 9708 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.12), residues: 3036 helix: -1.58 (0.13), residues: 1272 sheet: -3.39 (0.35), residues: 144 loop : -3.41 (0.11), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 22 HIS 0.001 0.000 HIS I 57 PHE 0.011 0.002 PHE L 64 TYR 0.012 0.002 TYR L 273 ARG 0.007 0.001 ARG L 16 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 490 time to evaluate : 2.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8329 (pptt) cc_final: 0.7836 (pptt) REVERT: E 45 LYS cc_start: 0.8272 (pptt) cc_final: 0.7783 (pptt) REVERT: E 155 ASN cc_start: 0.8270 (t0) cc_final: 0.8022 (t0) REVERT: H 45 LYS cc_start: 0.8037 (pptt) cc_final: 0.7702 (pptt) REVERT: H 207 TYR cc_start: 0.8691 (t80) cc_final: 0.7627 (t80) REVERT: J 69 MET cc_start: 0.7164 (ttt) cc_final: 0.6883 (tmm) REVERT: K 45 LYS cc_start: 0.8272 (pptt) cc_final: 0.8016 (pptt) REVERT: K 207 TYR cc_start: 0.8806 (t80) cc_final: 0.7950 (t80) outliers start: 0 outliers final: 0 residues processed: 490 average time/residue: 0.3997 time to fit residues: 296.7256 Evaluate side-chains 380 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 3.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 0.8980 chunk 227 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 153 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 235 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 142 optimal weight: 0.7980 chunk 175 optimal weight: 3.9990 chunk 272 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 271 ASN B 36 GLN B 271 ASN C 36 GLN D 36 GLN D 271 ASN E 36 GLN E 271 ASN F 36 GLN F 271 ASN G 36 GLN G 58 GLN G 155 ASN G 271 ASN H 36 GLN H 271 ASN I 36 GLN I 271 ASN J 36 GLN J 271 ASN ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 271 ASN L 36 GLN L 271 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 26052 Z= 0.150 Angle : 0.512 6.975 35232 Z= 0.264 Chirality : 0.043 0.143 3684 Planarity : 0.003 0.034 4536 Dihedral : 3.839 18.265 3432 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.37 % Allowed : 6.56 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.14), residues: 3036 helix: -0.22 (0.15), residues: 1296 sheet: -2.97 (0.36), residues: 144 loop : -2.55 (0.13), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 40 HIS 0.001 0.000 HIS J 57 PHE 0.009 0.001 PHE A 216 TYR 0.015 0.001 TYR G 92 ARG 0.002 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 444 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8180 (pptt) cc_final: 0.7558 (pttp) REVERT: B 45 LYS cc_start: 0.8162 (pptt) cc_final: 0.7856 (pttp) REVERT: C 85 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7747 (mm) REVERT: C 214 MET cc_start: 0.7277 (mmm) cc_final: 0.6999 (mmm) REVERT: D 45 LYS cc_start: 0.8133 (pptt) cc_final: 0.7614 (pttp) REVERT: E 45 LYS cc_start: 0.8160 (pptt) cc_final: 0.7843 (pttp) REVERT: F 45 LYS cc_start: 0.8144 (pptt) cc_final: 0.7721 (pttp) REVERT: F 145 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7815 (mt-10) REVERT: H 73 LEU cc_start: 0.7934 (tp) cc_final: 0.7680 (tt) REVERT: H 207 TYR cc_start: 0.8955 (t80) cc_final: 0.8202 (t80) REVERT: J 45 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7625 (pttp) REVERT: K 45 LYS cc_start: 0.8176 (pptt) cc_final: 0.7773 (pptt) REVERT: L 85 LEU cc_start: 0.8211 (tp) cc_final: 0.7897 (mm) outliers start: 10 outliers final: 3 residues processed: 446 average time/residue: 0.4222 time to fit residues: 280.7415 Evaluate side-chains 394 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 389 time to evaluate : 2.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain J residue 45 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 226 optimal weight: 0.8980 chunk 185 optimal weight: 8.9990 chunk 75 optimal weight: 0.0010 chunk 272 optimal weight: 6.9990 chunk 294 optimal weight: 5.9990 chunk 243 optimal weight: 0.7980 chunk 270 optimal weight: 1.9990 chunk 93 optimal weight: 0.3980 chunk 218 optimal weight: 0.5980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 26052 Z= 0.123 Angle : 0.450 4.720 35232 Z= 0.237 Chirality : 0.041 0.146 3684 Planarity : 0.003 0.029 4536 Dihedral : 3.623 18.088 3432 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.85 % Allowed : 7.48 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.15), residues: 3036 helix: 0.28 (0.15), residues: 1308 sheet: -2.78 (0.35), residues: 144 loop : -1.99 (0.14), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 40 HIS 0.001 0.000 HIS D 57 PHE 0.008 0.001 PHE G 216 TYR 0.014 0.001 TYR G 92 ARG 0.003 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 422 time to evaluate : 2.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.9068 (tt) cc_final: 0.8846 (tp) REVERT: A 37 MET cc_start: 0.8449 (ttm) cc_final: 0.8222 (ttm) REVERT: A 45 LYS cc_start: 0.8125 (pptt) cc_final: 0.7582 (pttp) REVERT: A 109 ASP cc_start: 0.6609 (t0) cc_final: 0.6127 (t0) REVERT: B 45 LYS cc_start: 0.8203 (pptt) cc_final: 0.7673 (pptt) REVERT: B 85 LEU cc_start: 0.7881 (tp) cc_final: 0.7469 (mm) REVERT: B 110 MET cc_start: 0.6826 (ptp) cc_final: 0.6221 (ptp) REVERT: B 114 LEU cc_start: 0.2464 (OUTLIER) cc_final: 0.1720 (pp) REVERT: C 114 LEU cc_start: 0.2920 (OUTLIER) cc_final: 0.2605 (pp) REVERT: C 214 MET cc_start: 0.7408 (mmm) cc_final: 0.7103 (mmm) REVERT: D 45 LYS cc_start: 0.8049 (pptt) cc_final: 0.7530 (pttp) REVERT: E 45 LYS cc_start: 0.8071 (pptt) cc_final: 0.7685 (pttp) REVERT: E 114 LEU cc_start: 0.2091 (OUTLIER) cc_final: 0.1415 (pp) REVERT: F 114 LEU cc_start: 0.2612 (OUTLIER) cc_final: 0.2146 (pp) REVERT: F 145 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7808 (mt-10) REVERT: G 45 LYS cc_start: 0.8296 (pttp) cc_final: 0.7988 (pttp) REVERT: G 70 TYR cc_start: 0.6529 (m-80) cc_final: 0.6135 (m-80) REVERT: G 114 LEU cc_start: 0.2228 (OUTLIER) cc_final: 0.1485 (pp) REVERT: H 73 LEU cc_start: 0.7858 (tp) cc_final: 0.7635 (tt) REVERT: H 114 LEU cc_start: 0.2548 (OUTLIER) cc_final: 0.1854 (pp) REVERT: I 114 LEU cc_start: 0.3203 (OUTLIER) cc_final: 0.2675 (pp) REVERT: I 145 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7742 (mt-10) REVERT: J 43 LEU cc_start: 0.8814 (mp) cc_final: 0.8588 (mt) REVERT: J 45 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7694 (pttp) REVERT: K 45 LYS cc_start: 0.8160 (pptt) cc_final: 0.7712 (pptt) REVERT: K 85 LEU cc_start: 0.7955 (tp) cc_final: 0.7577 (mm) REVERT: K 114 LEU cc_start: 0.2782 (OUTLIER) cc_final: 0.1975 (pp) REVERT: L 85 LEU cc_start: 0.8270 (tp) cc_final: 0.7977 (mm) REVERT: L 114 LEU cc_start: 0.3193 (OUTLIER) cc_final: 0.2687 (pp) outliers start: 23 outliers final: 5 residues processed: 438 average time/residue: 0.4051 time to fit residues: 266.3152 Evaluate side-chains 402 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 387 time to evaluate : 2.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 141 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 0.9980 chunk 205 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 183 optimal weight: 0.4980 chunk 273 optimal weight: 0.9980 chunk 289 optimal weight: 1.9990 chunk 143 optimal weight: 0.0370 chunk 259 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 26052 Z= 0.132 Angle : 0.454 6.189 35232 Z= 0.237 Chirality : 0.042 0.155 3684 Planarity : 0.002 0.027 4536 Dihedral : 3.595 18.369 3432 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.11 % Allowed : 8.26 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.15), residues: 3036 helix: 0.69 (0.15), residues: 1296 sheet: -2.75 (0.35), residues: 144 loop : -1.66 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 107 HIS 0.001 0.000 HIS G 57 PHE 0.012 0.001 PHE G 64 TYR 0.028 0.001 TYR G 92 ARG 0.002 0.000 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 399 time to evaluate : 2.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLN cc_start: 0.7821 (pt0) cc_final: 0.7511 (pp30) REVERT: A 45 LYS cc_start: 0.8203 (pptt) cc_final: 0.7692 (pttp) REVERT: B 45 LYS cc_start: 0.8309 (pptt) cc_final: 0.7749 (pptt) REVERT: B 85 LEU cc_start: 0.8008 (tp) cc_final: 0.7616 (mm) REVERT: B 110 MET cc_start: 0.6725 (ptp) cc_final: 0.6197 (ptp) REVERT: B 114 LEU cc_start: 0.2466 (OUTLIER) cc_final: 0.1721 (pp) REVERT: C 45 LYS cc_start: 0.8146 (pptt) cc_final: 0.7686 (pttp) REVERT: C 85 LEU cc_start: 0.8219 (tp) cc_final: 0.7948 (mm) REVERT: C 114 LEU cc_start: 0.2888 (OUTLIER) cc_final: 0.2312 (pp) REVERT: C 214 MET cc_start: 0.7559 (mmm) cc_final: 0.7176 (mmm) REVERT: D 45 LYS cc_start: 0.8169 (pptt) cc_final: 0.7689 (pttp) REVERT: E 45 LYS cc_start: 0.8083 (pptt) cc_final: 0.7716 (pttp) REVERT: E 114 LEU cc_start: 0.2209 (OUTLIER) cc_final: 0.1528 (pp) REVERT: E 224 MET cc_start: 0.8454 (mmp) cc_final: 0.8204 (mmp) REVERT: F 45 LYS cc_start: 0.8121 (pptt) cc_final: 0.7688 (pttp) REVERT: F 114 LEU cc_start: 0.3002 (OUTLIER) cc_final: 0.2597 (pp) REVERT: G 36 GLN cc_start: 0.7948 (pt0) cc_final: 0.7597 (pp30) REVERT: G 45 LYS cc_start: 0.8321 (pttp) cc_final: 0.7987 (pttp) REVERT: H 92 TYR cc_start: 0.8045 (t80) cc_final: 0.7744 (t80) REVERT: H 114 LEU cc_start: 0.2437 (OUTLIER) cc_final: 0.1435 (pp) REVERT: H 224 MET cc_start: 0.8546 (mmp) cc_final: 0.8209 (mmp) REVERT: I 45 LYS cc_start: 0.8146 (pptt) cc_final: 0.7693 (pttp) REVERT: I 114 LEU cc_start: 0.2978 (OUTLIER) cc_final: 0.2564 (pp) REVERT: J 45 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7810 (pttp) REVERT: K 36 GLN cc_start: 0.7963 (pt0) cc_final: 0.7578 (pp30) REVERT: K 45 LYS cc_start: 0.8234 (pptt) cc_final: 0.7726 (pptt) REVERT: K 85 LEU cc_start: 0.8049 (tp) cc_final: 0.7689 (mm) REVERT: K 114 LEU cc_start: 0.2764 (OUTLIER) cc_final: 0.1953 (pp) REVERT: K 224 MET cc_start: 0.8533 (mmp) cc_final: 0.8199 (mmp) REVERT: L 85 LEU cc_start: 0.8305 (tp) cc_final: 0.8034 (mm) REVERT: L 114 LEU cc_start: 0.3099 (OUTLIER) cc_final: 0.2638 (pp) REVERT: L 181 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7002 (mt-10) outliers start: 30 outliers final: 10 residues processed: 421 average time/residue: 0.4081 time to fit residues: 258.1372 Evaluate side-chains 398 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 378 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 272 GLU Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 181 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 5.9990 chunk 164 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 247 optimal weight: 10.0000 chunk 200 optimal weight: 0.0370 chunk 0 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26052 Z= 0.191 Angle : 0.477 7.126 35232 Z= 0.251 Chirality : 0.043 0.158 3684 Planarity : 0.002 0.025 4536 Dihedral : 3.721 18.204 3432 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.44 % Allowed : 8.63 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.15), residues: 3036 helix: 0.89 (0.15), residues: 1284 sheet: -2.76 (0.36), residues: 144 loop : -1.38 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 107 HIS 0.001 0.000 HIS F 57 PHE 0.013 0.001 PHE I 64 TYR 0.013 0.001 TYR H 108 ARG 0.004 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 404 time to evaluate : 2.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8258 (pptt) cc_final: 0.7729 (pttp) REVERT: B 85 LEU cc_start: 0.8130 (tp) cc_final: 0.7845 (mm) REVERT: B 110 MET cc_start: 0.6737 (ptp) cc_final: 0.6347 (ptp) REVERT: B 114 LEU cc_start: 0.2622 (OUTLIER) cc_final: 0.1887 (pp) REVERT: C 45 LYS cc_start: 0.8178 (pptt) cc_final: 0.7778 (pttp) REVERT: C 85 LEU cc_start: 0.8347 (tp) cc_final: 0.8101 (mm) REVERT: C 114 LEU cc_start: 0.3080 (OUTLIER) cc_final: 0.2511 (pp) REVERT: C 214 MET cc_start: 0.7653 (mmm) cc_final: 0.7343 (mmm) REVERT: D 45 LYS cc_start: 0.8257 (pptt) cc_final: 0.7760 (pttp) REVERT: D 109 ASP cc_start: 0.6587 (t0) cc_final: 0.6348 (t0) REVERT: E 45 LYS cc_start: 0.8160 (pptt) cc_final: 0.7670 (pptt) REVERT: E 85 LEU cc_start: 0.8115 (tp) cc_final: 0.7738 (mm) REVERT: E 114 LEU cc_start: 0.2311 (OUTLIER) cc_final: 0.1624 (pp) REVERT: F 45 LYS cc_start: 0.8176 (pptt) cc_final: 0.7785 (pttp) REVERT: F 114 LEU cc_start: 0.3076 (OUTLIER) cc_final: 0.2363 (pp) REVERT: G 45 LYS cc_start: 0.8385 (pttp) cc_final: 0.8059 (pttp) REVERT: G 86 TYR cc_start: 0.8570 (m-10) cc_final: 0.8313 (m-10) REVERT: H 114 LEU cc_start: 0.2790 (OUTLIER) cc_final: 0.1750 (pp) REVERT: I 45 LYS cc_start: 0.8171 (pptt) cc_final: 0.7791 (pttp) REVERT: I 114 LEU cc_start: 0.3032 (OUTLIER) cc_final: 0.2279 (pp) REVERT: J 45 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7850 (pttp) REVERT: K 45 LYS cc_start: 0.8211 (pptt) cc_final: 0.7905 (pttp) REVERT: K 85 LEU cc_start: 0.8164 (tp) cc_final: 0.7838 (mm) REVERT: K 114 LEU cc_start: 0.2699 (OUTLIER) cc_final: 0.1901 (pp) REVERT: L 45 LYS cc_start: 0.8203 (pptt) cc_final: 0.7791 (pttp) REVERT: L 85 LEU cc_start: 0.8407 (tp) cc_final: 0.8148 (mm) REVERT: L 114 LEU cc_start: 0.3100 (OUTLIER) cc_final: 0.2358 (pp) outliers start: 39 outliers final: 13 residues processed: 428 average time/residue: 0.4251 time to fit residues: 271.8673 Evaluate side-chains 396 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 374 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain J residue 37 MET Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 272 GLU Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 181 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 0.0870 chunk 261 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 290 optimal weight: 0.8980 chunk 240 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 96 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26052 Z= 0.156 Angle : 0.466 6.038 35232 Z= 0.245 Chirality : 0.042 0.153 3684 Planarity : 0.002 0.025 4536 Dihedral : 3.686 18.447 3432 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.00 % Allowed : 9.63 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 3036 helix: 1.04 (0.15), residues: 1284 sheet: -2.72 (0.37), residues: 144 loop : -1.23 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 22 HIS 0.001 0.000 HIS G 57 PHE 0.010 0.001 PHE C 64 TYR 0.015 0.001 TYR H 92 ARG 0.002 0.000 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 395 time to evaluate : 2.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8245 (pptt) cc_final: 0.7777 (pttp) REVERT: B 85 LEU cc_start: 0.8242 (tp) cc_final: 0.7970 (mm) REVERT: B 110 MET cc_start: 0.6844 (ptp) cc_final: 0.6469 (ptp) REVERT: B 114 LEU cc_start: 0.2690 (OUTLIER) cc_final: 0.1973 (pp) REVERT: C 45 LYS cc_start: 0.8169 (pptt) cc_final: 0.7756 (pttp) REVERT: C 114 LEU cc_start: 0.3007 (OUTLIER) cc_final: 0.2500 (pp) REVERT: C 214 MET cc_start: 0.7602 (mmm) cc_final: 0.7294 (mmm) REVERT: D 45 LYS cc_start: 0.8213 (pptt) cc_final: 0.7774 (pttp) REVERT: D 109 ASP cc_start: 0.6578 (t0) cc_final: 0.6337 (t0) REVERT: E 45 LYS cc_start: 0.8068 (pptt) cc_final: 0.7654 (pptt) REVERT: E 114 LEU cc_start: 0.2380 (OUTLIER) cc_final: 0.1745 (pp) REVERT: F 45 LYS cc_start: 0.8161 (pptt) cc_final: 0.7813 (pttp) REVERT: F 114 LEU cc_start: 0.3055 (OUTLIER) cc_final: 0.2407 (pp) REVERT: G 45 LYS cc_start: 0.8344 (pttp) cc_final: 0.8026 (pttp) REVERT: G 70 TYR cc_start: 0.6650 (m-80) cc_final: 0.6417 (m-80) REVERT: H 85 LEU cc_start: 0.8081 (tp) cc_final: 0.7693 (mm) REVERT: H 92 TYR cc_start: 0.7860 (t80) cc_final: 0.7592 (t80) REVERT: H 114 LEU cc_start: 0.2677 (OUTLIER) cc_final: 0.1820 (pp) REVERT: I 45 LYS cc_start: 0.8170 (pptt) cc_final: 0.7787 (pttp) REVERT: I 114 LEU cc_start: 0.3100 (OUTLIER) cc_final: 0.2414 (pp) REVERT: J 45 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7600 (pttp) REVERT: K 45 LYS cc_start: 0.8139 (pptt) cc_final: 0.7821 (pttp) REVERT: K 85 LEU cc_start: 0.8050 (tp) cc_final: 0.7685 (mm) REVERT: K 114 LEU cc_start: 0.2653 (OUTLIER) cc_final: 0.1934 (pp) REVERT: L 45 LYS cc_start: 0.8198 (pptt) cc_final: 0.7799 (pttp) REVERT: L 85 LEU cc_start: 0.8436 (tp) cc_final: 0.8214 (mm) REVERT: L 114 LEU cc_start: 0.3085 (OUTLIER) cc_final: 0.2410 (pp) outliers start: 27 outliers final: 14 residues processed: 415 average time/residue: 0.4259 time to fit residues: 262.8071 Evaluate side-chains 391 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 368 time to evaluate : 2.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 181 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 211 optimal weight: 0.9990 chunk 164 optimal weight: 0.7980 chunk 244 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 chunk 289 optimal weight: 0.6980 chunk 180 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26052 Z= 0.145 Angle : 0.462 8.514 35232 Z= 0.243 Chirality : 0.042 0.144 3684 Planarity : 0.002 0.025 4536 Dihedral : 3.633 18.681 3432 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.15 % Allowed : 10.37 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 3036 helix: 1.15 (0.15), residues: 1296 sheet: -2.69 (0.37), residues: 144 loop : -1.24 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 22 HIS 0.001 0.000 HIS G 57 PHE 0.009 0.001 PHE G 64 TYR 0.016 0.001 TYR B 108 ARG 0.003 0.000 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 395 time to evaluate : 3.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7605 (mtp180) cc_final: 0.7397 (mtp180) REVERT: A 45 LYS cc_start: 0.8233 (pptt) cc_final: 0.7709 (pttp) REVERT: B 83 ILE cc_start: 0.8786 (pt) cc_final: 0.8568 (pt) REVERT: B 85 LEU cc_start: 0.8251 (tp) cc_final: 0.7953 (mm) REVERT: B 110 MET cc_start: 0.6946 (ptp) cc_final: 0.6620 (ptp) REVERT: B 114 LEU cc_start: 0.2695 (OUTLIER) cc_final: 0.2013 (pp) REVERT: C 45 LYS cc_start: 0.8179 (pptt) cc_final: 0.7792 (pttp) REVERT: C 114 LEU cc_start: 0.2842 (OUTLIER) cc_final: 0.2343 (pp) REVERT: C 214 MET cc_start: 0.7590 (mmm) cc_final: 0.7268 (mmm) REVERT: D 45 LYS cc_start: 0.8195 (pptt) cc_final: 0.7763 (pttp) REVERT: D 109 ASP cc_start: 0.6477 (t0) cc_final: 0.6228 (t0) REVERT: E 45 LYS cc_start: 0.8071 (pptt) cc_final: 0.7640 (pptt) REVERT: E 85 LEU cc_start: 0.8147 (tp) cc_final: 0.7774 (mm) REVERT: E 114 LEU cc_start: 0.2504 (OUTLIER) cc_final: 0.1906 (pp) REVERT: F 45 LYS cc_start: 0.8186 (pptt) cc_final: 0.7821 (pttp) REVERT: F 114 LEU cc_start: 0.3078 (OUTLIER) cc_final: 0.2474 (pp) REVERT: G 45 LYS cc_start: 0.8295 (pttp) cc_final: 0.7984 (pttp) REVERT: G 70 TYR cc_start: 0.6728 (m-80) cc_final: 0.6458 (m-80) REVERT: H 45 LYS cc_start: 0.8082 (pptt) cc_final: 0.7590 (pptt) REVERT: H 85 LEU cc_start: 0.8103 (tp) cc_final: 0.7717 (mm) REVERT: H 114 LEU cc_start: 0.2670 (OUTLIER) cc_final: 0.1952 (pp) REVERT: I 45 LYS cc_start: 0.8140 (pptt) cc_final: 0.7794 (pttp) REVERT: I 114 LEU cc_start: 0.3146 (OUTLIER) cc_final: 0.2499 (pp) REVERT: J 45 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7853 (pttp) REVERT: J 70 TYR cc_start: 0.6782 (m-80) cc_final: 0.6541 (m-80) REVERT: J 109 ASP cc_start: 0.6558 (t0) cc_final: 0.6075 (t0) REVERT: K 45 LYS cc_start: 0.8128 (pptt) cc_final: 0.7605 (pptt) REVERT: K 85 LEU cc_start: 0.8240 (tp) cc_final: 0.7861 (mm) REVERT: K 114 LEU cc_start: 0.2635 (OUTLIER) cc_final: 0.1954 (pp) REVERT: L 45 LYS cc_start: 0.8137 (pptt) cc_final: 0.7749 (pttp) REVERT: L 85 LEU cc_start: 0.8514 (tp) cc_final: 0.8279 (mm) REVERT: L 114 LEU cc_start: 0.3173 (OUTLIER) cc_final: 0.2513 (pp) REVERT: L 181 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7049 (tt0) outliers start: 31 outliers final: 14 residues processed: 416 average time/residue: 0.4285 time to fit residues: 266.2003 Evaluate side-chains 379 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 355 time to evaluate : 2.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain J residue 37 MET Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 181 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 0.2980 chunk 115 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 196 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 227 optimal weight: 0.6980 chunk 263 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN C 82 GLN E 82 GLN F 82 GLN I 82 GLN K 82 GLN L 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26052 Z= 0.282 Angle : 0.536 8.067 35232 Z= 0.281 Chirality : 0.045 0.159 3684 Planarity : 0.003 0.026 4536 Dihedral : 3.937 18.803 3432 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.19 % Allowed : 10.89 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.15), residues: 3036 helix: 1.14 (0.15), residues: 1284 sheet: -2.75 (0.38), residues: 144 loop : -1.14 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 22 HIS 0.002 0.001 HIS F 57 PHE 0.018 0.002 PHE F 64 TYR 0.015 0.001 TYR H 92 ARG 0.003 0.000 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 366 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8346 (pptt) cc_final: 0.7807 (pttp) REVERT: B 45 LYS cc_start: 0.8200 (pptt) cc_final: 0.7639 (pptt) REVERT: B 85 LEU cc_start: 0.8245 (tp) cc_final: 0.7859 (mm) REVERT: B 114 LEU cc_start: 0.2827 (OUTLIER) cc_final: 0.2111 (pp) REVERT: C 114 LEU cc_start: 0.2933 (OUTLIER) cc_final: 0.2386 (pp) REVERT: C 214 MET cc_start: 0.7691 (mmm) cc_final: 0.7423 (mmm) REVERT: D 45 LYS cc_start: 0.8240 (pptt) cc_final: 0.7846 (pttp) REVERT: E 45 LYS cc_start: 0.8194 (pptt) cc_final: 0.7729 (pptt) REVERT: E 85 LEU cc_start: 0.8274 (tp) cc_final: 0.7884 (mm) REVERT: E 114 LEU cc_start: 0.2592 (OUTLIER) cc_final: 0.1922 (pp) REVERT: E 229 LEU cc_start: 0.8461 (mp) cc_final: 0.8230 (mp) REVERT: F 45 LYS cc_start: 0.8338 (pptt) cc_final: 0.7992 (pptt) REVERT: F 114 LEU cc_start: 0.3030 (OUTLIER) cc_final: 0.2396 (pp) REVERT: G 70 TYR cc_start: 0.6750 (m-80) cc_final: 0.6442 (m-80) REVERT: H 45 LYS cc_start: 0.8201 (pptt) cc_final: 0.7625 (pptt) REVERT: H 114 LEU cc_start: 0.2649 (OUTLIER) cc_final: 0.1861 (pp) REVERT: I 45 LYS cc_start: 0.8253 (pptt) cc_final: 0.7916 (pttp) REVERT: I 114 LEU cc_start: 0.3192 (OUTLIER) cc_final: 0.2524 (pp) REVERT: J 45 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8152 (pttp) REVERT: J 85 LEU cc_start: 0.8573 (tp) cc_final: 0.8109 (mm) REVERT: K 45 LYS cc_start: 0.8238 (pptt) cc_final: 0.7680 (pptt) REVERT: K 85 LEU cc_start: 0.8385 (tp) cc_final: 0.8071 (mm) REVERT: K 114 LEU cc_start: 0.2873 (OUTLIER) cc_final: 0.2114 (pp) REVERT: K 229 LEU cc_start: 0.8399 (mp) cc_final: 0.8164 (mp) REVERT: L 114 LEU cc_start: 0.3257 (OUTLIER) cc_final: 0.2579 (pp) REVERT: L 181 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7064 (tt0) outliers start: 32 outliers final: 14 residues processed: 389 average time/residue: 0.4484 time to fit residues: 255.8203 Evaluate side-chains 358 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 334 time to evaluate : 2.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain G residue 69 MET Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain J residue 37 MET Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 181 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 0.7980 chunk 252 optimal weight: 4.9990 chunk 269 optimal weight: 0.9980 chunk 276 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 211 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 243 optimal weight: 0.9990 chunk 254 optimal weight: 1.9990 chunk 268 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN E 82 GLN F 82 GLN I 82 GLN K 82 GLN L 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26052 Z= 0.161 Angle : 0.488 8.788 35232 Z= 0.256 Chirality : 0.042 0.154 3684 Planarity : 0.003 0.025 4536 Dihedral : 3.796 19.532 3432 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.30 % Allowed : 10.70 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.15), residues: 3036 helix: 1.24 (0.15), residues: 1284 sheet: -2.75 (0.38), residues: 144 loop : -1.02 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 40 HIS 0.001 0.000 HIS G 57 PHE 0.011 0.001 PHE C 64 TYR 0.016 0.001 TYR B 108 ARG 0.003 0.000 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 355 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8327 (pptt) cc_final: 0.7804 (pttp) REVERT: A 70 TYR cc_start: 0.6803 (m-80) cc_final: 0.6554 (m-80) REVERT: A 85 LEU cc_start: 0.8512 (tp) cc_final: 0.8049 (mm) REVERT: B 45 LYS cc_start: 0.8152 (pptt) cc_final: 0.7630 (pptt) REVERT: B 85 LEU cc_start: 0.8259 (tp) cc_final: 0.7894 (mm) REVERT: B 114 LEU cc_start: 0.2755 (OUTLIER) cc_final: 0.2059 (pp) REVERT: C 114 LEU cc_start: 0.2812 (OUTLIER) cc_final: 0.2304 (pp) REVERT: C 214 MET cc_start: 0.7600 (mmm) cc_final: 0.7324 (mmm) REVERT: D 45 LYS cc_start: 0.8258 (pptt) cc_final: 0.7849 (pttp) REVERT: D 70 TYR cc_start: 0.6710 (m-80) cc_final: 0.6500 (m-80) REVERT: E 45 LYS cc_start: 0.8140 (pptt) cc_final: 0.7641 (pptt) REVERT: E 114 LEU cc_start: 0.2532 (OUTLIER) cc_final: 0.1918 (pp) REVERT: E 229 LEU cc_start: 0.8443 (mp) cc_final: 0.8225 (mp) REVERT: F 45 LYS cc_start: 0.8288 (pptt) cc_final: 0.7917 (pptt) REVERT: F 114 LEU cc_start: 0.3004 (OUTLIER) cc_final: 0.2421 (pp) REVERT: G 45 LYS cc_start: 0.8328 (pttp) cc_final: 0.8069 (pttp) REVERT: G 70 TYR cc_start: 0.6733 (m-80) cc_final: 0.6437 (m-80) REVERT: H 85 LEU cc_start: 0.8264 (tp) cc_final: 0.7860 (mm) REVERT: H 114 LEU cc_start: 0.2754 (OUTLIER) cc_final: 0.2067 (pp) REVERT: I 45 LYS cc_start: 0.8241 (pptt) cc_final: 0.7889 (pttp) REVERT: I 114 LEU cc_start: 0.3137 (OUTLIER) cc_final: 0.2530 (pp) REVERT: J 45 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7976 (pttp) REVERT: J 70 TYR cc_start: 0.6795 (m-80) cc_final: 0.6553 (m-80) REVERT: J 85 LEU cc_start: 0.8565 (tp) cc_final: 0.8113 (mm) REVERT: K 45 LYS cc_start: 0.8194 (pptt) cc_final: 0.7666 (pptt) REVERT: K 85 LEU cc_start: 0.8257 (tp) cc_final: 0.7905 (mm) REVERT: K 114 LEU cc_start: 0.2776 (OUTLIER) cc_final: 0.1976 (pp) REVERT: K 229 LEU cc_start: 0.8330 (mp) cc_final: 0.8087 (mp) REVERT: L 114 LEU cc_start: 0.3192 (OUTLIER) cc_final: 0.2546 (pp) REVERT: L 181 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7062 (tt0) outliers start: 35 outliers final: 21 residues processed: 381 average time/residue: 0.4563 time to fit residues: 253.4889 Evaluate side-chains 374 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 343 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain G residue 69 MET Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 82 GLN Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain J residue 37 MET Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 82 GLN Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 181 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 3.9990 chunk 284 optimal weight: 0.9980 chunk 173 optimal weight: 0.3980 chunk 135 optimal weight: 10.0000 chunk 198 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 chunk 237 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 183 optimal weight: 0.9980 chunk 145 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN E 82 GLN F 82 GLN I 82 GLN J 82 GLN K 82 GLN L 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26052 Z= 0.151 Angle : 0.485 8.523 35232 Z= 0.254 Chirality : 0.042 0.157 3684 Planarity : 0.003 0.026 4536 Dihedral : 3.714 19.329 3432 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.19 % Allowed : 10.78 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 3036 helix: 1.34 (0.15), residues: 1284 sheet: -2.67 (0.38), residues: 144 loop : -0.95 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 22 HIS 0.001 0.000 HIS G 57 PHE 0.009 0.001 PHE C 64 TYR 0.021 0.001 TYR H 92 ARG 0.002 0.000 ARG A 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 356 time to evaluate : 3.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8338 (pptt) cc_final: 0.7851 (pttp) REVERT: A 70 TYR cc_start: 0.6799 (m-80) cc_final: 0.6544 (m-80) REVERT: A 85 LEU cc_start: 0.8518 (tp) cc_final: 0.8117 (mm) REVERT: B 45 LYS cc_start: 0.8150 (pptt) cc_final: 0.7629 (pptt) REVERT: B 114 LEU cc_start: 0.2751 (OUTLIER) cc_final: 0.2054 (pp) REVERT: C 114 LEU cc_start: 0.2811 (OUTLIER) cc_final: 0.2302 (pp) REVERT: C 214 MET cc_start: 0.7588 (mmm) cc_final: 0.7313 (mmm) REVERT: D 45 LYS cc_start: 0.8248 (pptt) cc_final: 0.7857 (pttp) REVERT: E 45 LYS cc_start: 0.8141 (pptt) cc_final: 0.7652 (pptt) REVERT: E 85 LEU cc_start: 0.8281 (tp) cc_final: 0.7927 (mm) REVERT: E 114 LEU cc_start: 0.2530 (OUTLIER) cc_final: 0.1929 (pp) REVERT: E 229 LEU cc_start: 0.8396 (mp) cc_final: 0.8179 (mp) REVERT: F 45 LYS cc_start: 0.8256 (pptt) cc_final: 0.7909 (pptt) REVERT: F 114 LEU cc_start: 0.3065 (OUTLIER) cc_final: 0.2511 (pp) REVERT: G 45 LYS cc_start: 0.8268 (pttp) cc_final: 0.8054 (pttp) REVERT: G 70 TYR cc_start: 0.6756 (m-80) cc_final: 0.6447 (m-80) REVERT: H 45 LYS cc_start: 0.8137 (pptt) cc_final: 0.7584 (pptt) REVERT: H 114 LEU cc_start: 0.2742 (OUTLIER) cc_final: 0.2075 (pp) REVERT: I 45 LYS cc_start: 0.8257 (pptt) cc_final: 0.7899 (pttp) REVERT: I 114 LEU cc_start: 0.3169 (OUTLIER) cc_final: 0.2561 (pp) REVERT: J 45 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7944 (pttp) REVERT: J 70 TYR cc_start: 0.6790 (m-80) cc_final: 0.6547 (m-80) REVERT: J 85 LEU cc_start: 0.8569 (tp) cc_final: 0.8130 (mm) REVERT: K 45 LYS cc_start: 0.8194 (pptt) cc_final: 0.7659 (pptt) REVERT: K 85 LEU cc_start: 0.8357 (tp) cc_final: 0.8003 (mm) REVERT: K 110 MET cc_start: 0.7155 (ptm) cc_final: 0.6792 (ptp) REVERT: K 114 LEU cc_start: 0.2876 (OUTLIER) cc_final: 0.2236 (pp) REVERT: K 229 LEU cc_start: 0.8340 (mp) cc_final: 0.8123 (mp) REVERT: L 114 LEU cc_start: 0.3160 (OUTLIER) cc_final: 0.2548 (pp) REVERT: L 181 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7073 (tt0) outliers start: 32 outliers final: 19 residues processed: 381 average time/residue: 0.4703 time to fit residues: 260.1649 Evaluate side-chains 365 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 336 time to evaluate : 4.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain G residue 69 MET Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 82 GLN Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain J residue 37 MET Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 82 GLN Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 181 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 0.0770 chunk 253 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 219 optimal weight: 0.0570 chunk 35 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 244 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN J 82 GLN K 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.148459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.117026 restraints weight = 34324.217| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.19 r_work: 0.3243 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26052 Z= 0.129 Angle : 0.476 9.782 35232 Z= 0.248 Chirality : 0.041 0.167 3684 Planarity : 0.003 0.026 4536 Dihedral : 3.645 19.464 3432 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.15 % Allowed : 11.19 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 3036 helix: 1.44 (0.15), residues: 1284 sheet: -2.64 (0.38), residues: 144 loop : -0.89 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 22 HIS 0.001 0.000 HIS G 57 PHE 0.007 0.001 PHE D 64 TYR 0.016 0.001 TYR H 92 ARG 0.005 0.000 ARG I 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6030.73 seconds wall clock time: 107 minutes 34.69 seconds (6454.69 seconds total)