Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 12 10:04:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc0_25007/08_2023/7sc0_25007.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc0_25007/08_2023/7sc0_25007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc0_25007/08_2023/7sc0_25007.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc0_25007/08_2023/7sc0_25007.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc0_25007/08_2023/7sc0_25007.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc0_25007/08_2023/7sc0_25007.pdb" } resolution = 3.4 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= 0.039 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 44 5.16 5 C 7766 2.51 5 N 1826 2.21 5 O 2002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 76": "OE1" <-> "OE2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B GLU 161": "OE1" <-> "OE2" Residue "C GLU 76": "OE1" <-> "OE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "D GLU 161": "OE1" <-> "OE2" Residue "E GLU 76": "OE1" <-> "OE2" Residue "E GLU 161": "OE1" <-> "OE2" Residue "F GLU 76": "OE1" <-> "OE2" Residue "F GLU 161": "OE1" <-> "OE2" Residue "G GLU 76": "OE1" <-> "OE2" Residue "G GLU 161": "OE1" <-> "OE2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H GLU 161": "OE1" <-> "OE2" Residue "I GLU 76": "OE1" <-> "OE2" Residue "I GLU 161": "OE1" <-> "OE2" Residue "J GLU 76": "OE1" <-> "OE2" Residue "J GLU 161": "OE1" <-> "OE2" Residue "K GLU 76": "OE1" <-> "OE2" Residue "K GLU 161": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 11638 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1058 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "B" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1058 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "C" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1058 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "D" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1058 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "E" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1058 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "F" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1058 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "G" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1058 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "H" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1058 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1058 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "J" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1058 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1058 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Time building chain proxies: 5.54, per 1000 atoms: 0.48 Number of scatterers: 11638 At special positions: 0 Unit cell: (147.98, 148.96, 50.96, 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 44 16.00 O 2002 8.00 N 1826 7.00 C 7766 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 - 3.50 Amino acid : False - 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: 4.33 Conformation dependent library (CDL) restraints added in 1.6 seconds 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2728 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 1 sheets defined 72.1% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 81 through 107 removed outlier: 4.368A pdb=" N ALA A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE A 89 " --> pdb=" O TRP A 85 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 100 " --> pdb=" O LYS A 96 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG A 101 " --> pdb=" O TYR A 97 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 129 removed outlier: 3.703A pdb=" N ALA A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 113 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE A 114 " --> pdb=" O PRO A 110 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP A 115 " --> pdb=" O MET A 111 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 120 " --> pdb=" O GLY A 116 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 121 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 122 " --> pdb=" O TYR A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 141 removed outlier: 3.846A pdb=" N LEU A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU A 140 " --> pdb=" O SER A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 156 Processing helix chain 'A' and resid 158 through 163 removed outlier: 3.565A pdb=" N ALA A 162 " --> pdb=" O PRO A 158 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 158 through 163' Processing helix chain 'A' and resid 164 through 168 removed outlier: 4.036A pdb=" N PHE A 167 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 71 Processing helix chain 'B' and resid 81 through 107 removed outlier: 4.368A pdb=" N ALA B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE B 89 " --> pdb=" O TRP B 85 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG B 101 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 129 removed outlier: 3.704A pdb=" N ALA B 112 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 113 " --> pdb=" O ILE B 109 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE B 114 " --> pdb=" O PRO B 110 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRP B 115 " --> pdb=" O MET B 111 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 122 " --> pdb=" O TYR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 141 removed outlier: 3.846A pdb=" N LEU B 138 " --> pdb=" O ILE B 134 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE B 139 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU B 140 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 156 Processing helix chain 'B' and resid 158 through 163 removed outlier: 3.565A pdb=" N ALA B 162 " --> pdb=" O PRO B 158 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 158 through 163' Processing helix chain 'B' and resid 164 through 168 removed outlier: 4.037A pdb=" N PHE B 167 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 81 through 107 removed outlier: 4.368A pdb=" N ALA C 87 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE C 89 " --> pdb=" O TRP C 85 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS C 96 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG C 101 " --> pdb=" O TYR C 97 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE C 107 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 129 removed outlier: 3.704A pdb=" N ALA C 112 " --> pdb=" O GLY C 108 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 113 " --> pdb=" O ILE C 109 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE C 114 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRP C 115 " --> pdb=" O MET C 111 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 122 " --> pdb=" O TYR C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 141 removed outlier: 3.846A pdb=" N LEU C 138 " --> pdb=" O ILE C 134 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE C 139 " --> pdb=" O LYS C 135 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU C 140 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 156 Processing helix chain 'C' and resid 158 through 163 removed outlier: 3.564A pdb=" N ALA C 162 " --> pdb=" O PRO C 158 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL C 163 " --> pdb=" O LEU C 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 158 through 163' Processing helix chain 'C' and resid 164 through 168 removed outlier: 4.037A pdb=" N PHE C 167 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 81 through 107 removed outlier: 4.368A pdb=" N ALA D 87 " --> pdb=" O GLY D 83 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE D 89 " --> pdb=" O TRP D 85 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS D 96 " --> pdb=" O PHE D 92 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR D 100 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG D 101 " --> pdb=" O TYR D 97 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 129 removed outlier: 3.704A pdb=" N ALA D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU D 113 " --> pdb=" O ILE D 109 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE D 114 " --> pdb=" O PRO D 110 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRP D 115 " --> pdb=" O MET D 111 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA D 120 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE D 121 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 122 " --> pdb=" O TYR D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 141 removed outlier: 3.846A pdb=" N LEU D 138 " --> pdb=" O ILE D 134 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE D 139 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU D 140 " --> pdb=" O SER D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 156 Processing helix chain 'D' and resid 158 through 163 removed outlier: 3.565A pdb=" N ALA D 162 " --> pdb=" O PRO D 158 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 158 through 163' Processing helix chain 'D' and resid 164 through 168 removed outlier: 4.037A pdb=" N PHE D 167 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 71 Processing helix chain 'E' and resid 81 through 107 removed outlier: 4.368A pdb=" N ALA E 87 " --> pdb=" O GLY E 83 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE E 89 " --> pdb=" O TRP E 85 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR E 90 " --> pdb=" O LYS E 86 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS E 96 " --> pdb=" O PHE E 92 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR E 100 " --> pdb=" O LYS E 96 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG E 101 " --> pdb=" O TYR E 97 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE E 107 " --> pdb=" O LEU E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 129 removed outlier: 3.705A pdb=" N ALA E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE E 114 " --> pdb=" O PRO E 110 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRP E 115 " --> pdb=" O MET E 111 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA E 120 " --> pdb=" O GLY E 116 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE E 121 " --> pdb=" O ILE E 117 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU E 122 " --> pdb=" O TYR E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 141 removed outlier: 3.846A pdb=" N LEU E 138 " --> pdb=" O ILE E 134 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU E 140 " --> pdb=" O SER E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 156 Processing helix chain 'E' and resid 158 through 163 removed outlier: 3.564A pdb=" N ALA E 162 " --> pdb=" O PRO E 158 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 158 through 163' Processing helix chain 'E' and resid 164 through 168 removed outlier: 4.037A pdb=" N PHE E 167 " --> pdb=" O GLY E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 71 Processing helix chain 'F' and resid 81 through 107 removed outlier: 4.367A pdb=" N ALA F 87 " --> pdb=" O GLY F 83 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE F 89 " --> pdb=" O TRP F 85 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR F 90 " --> pdb=" O LYS F 86 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS F 96 " --> pdb=" O PHE F 92 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR F 100 " --> pdb=" O LYS F 96 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG F 101 " --> pdb=" O TYR F 97 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 129 removed outlier: 3.704A pdb=" N ALA F 112 " --> pdb=" O GLY F 108 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU F 113 " --> pdb=" O ILE F 109 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE F 114 " --> pdb=" O PRO F 110 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP F 115 " --> pdb=" O MET F 111 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA F 120 " --> pdb=" O GLY F 116 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE F 121 " --> pdb=" O ILE F 117 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU F 122 " --> pdb=" O TYR F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 141 removed outlier: 3.846A pdb=" N LEU F 138 " --> pdb=" O ILE F 134 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE F 139 " --> pdb=" O LYS F 135 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU F 140 " --> pdb=" O SER F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 156 Processing helix chain 'F' and resid 158 through 163 removed outlier: 3.565A pdb=" N ALA F 162 " --> pdb=" O PRO F 158 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL F 163 " --> pdb=" O LEU F 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 158 through 163' Processing helix chain 'F' and resid 164 through 168 removed outlier: 4.036A pdb=" N PHE F 167 " --> pdb=" O GLY F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 71 Processing helix chain 'G' and resid 81 through 107 removed outlier: 4.368A pdb=" N ALA G 87 " --> pdb=" O GLY G 83 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE G 89 " --> pdb=" O TRP G 85 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR G 90 " --> pdb=" O LYS G 86 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS G 96 " --> pdb=" O PHE G 92 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR G 100 " --> pdb=" O LYS G 96 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG G 101 " --> pdb=" O TYR G 97 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE G 107 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 129 removed outlier: 3.705A pdb=" N ALA G 112 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU G 113 " --> pdb=" O ILE G 109 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE G 114 " --> pdb=" O PRO G 110 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRP G 115 " --> pdb=" O MET G 111 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA G 120 " --> pdb=" O GLY G 116 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE G 121 " --> pdb=" O ILE G 117 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU G 122 " --> pdb=" O TYR G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 141 removed outlier: 3.846A pdb=" N LEU G 138 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE G 139 " --> pdb=" O LYS G 135 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU G 140 " --> pdb=" O SER G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 156 Processing helix chain 'G' and resid 158 through 163 removed outlier: 3.565A pdb=" N ALA G 162 " --> pdb=" O PRO G 158 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL G 163 " --> pdb=" O LEU G 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 158 through 163' Processing helix chain 'G' and resid 164 through 168 removed outlier: 4.037A pdb=" N PHE G 167 " --> pdb=" O GLY G 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 71 Processing helix chain 'H' and resid 81 through 107 removed outlier: 4.368A pdb=" N ALA H 87 " --> pdb=" O GLY H 83 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE H 89 " --> pdb=" O TRP H 85 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR H 90 " --> pdb=" O LYS H 86 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS H 96 " --> pdb=" O PHE H 92 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR H 100 " --> pdb=" O LYS H 96 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG H 101 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 129 removed outlier: 3.704A pdb=" N ALA H 112 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU H 113 " --> pdb=" O ILE H 109 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE H 114 " --> pdb=" O PRO H 110 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRP H 115 " --> pdb=" O MET H 111 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA H 120 " --> pdb=" O GLY H 116 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE H 121 " --> pdb=" O ILE H 117 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU H 122 " --> pdb=" O TYR H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 141 removed outlier: 3.846A pdb=" N LEU H 138 " --> pdb=" O ILE H 134 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE H 139 " --> pdb=" O LYS H 135 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU H 140 " --> pdb=" O SER H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 156 Processing helix chain 'H' and resid 158 through 163 removed outlier: 3.565A pdb=" N ALA H 162 " --> pdb=" O PRO H 158 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL H 163 " --> pdb=" O LEU H 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 158 through 163' Processing helix chain 'H' and resid 164 through 168 removed outlier: 4.037A pdb=" N PHE H 167 " --> pdb=" O GLY H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 71 Processing helix chain 'I' and resid 81 through 107 removed outlier: 4.368A pdb=" N ALA I 87 " --> pdb=" O GLY I 83 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE I 89 " --> pdb=" O TRP I 85 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR I 90 " --> pdb=" O LYS I 86 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS I 96 " --> pdb=" O PHE I 92 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR I 100 " --> pdb=" O LYS I 96 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG I 101 " --> pdb=" O TYR I 97 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE I 107 " --> pdb=" O LEU I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 129 removed outlier: 3.705A pdb=" N ALA I 112 " --> pdb=" O GLY I 108 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU I 113 " --> pdb=" O ILE I 109 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE I 114 " --> pdb=" O PRO I 110 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRP I 115 " --> pdb=" O MET I 111 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA I 120 " --> pdb=" O GLY I 116 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU I 122 " --> pdb=" O TYR I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 129 through 141 removed outlier: 3.845A pdb=" N LEU I 138 " --> pdb=" O ILE I 134 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE I 139 " --> pdb=" O LYS I 135 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU I 140 " --> pdb=" O SER I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 156 Processing helix chain 'I' and resid 158 through 163 removed outlier: 3.565A pdb=" N ALA I 162 " --> pdb=" O PRO I 158 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL I 163 " --> pdb=" O LEU I 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 158 through 163' Processing helix chain 'I' and resid 164 through 168 removed outlier: 4.038A pdb=" N PHE I 167 " --> pdb=" O GLY I 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 71 Processing helix chain 'J' and resid 81 through 107 removed outlier: 4.368A pdb=" N ALA J 87 " --> pdb=" O GLY J 83 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE J 89 " --> pdb=" O TRP J 85 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR J 90 " --> pdb=" O LYS J 86 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS J 96 " --> pdb=" O PHE J 92 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR J 100 " --> pdb=" O LYS J 96 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG J 101 " --> pdb=" O TYR J 97 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE J 107 " --> pdb=" O LEU J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 129 removed outlier: 3.704A pdb=" N ALA J 112 " --> pdb=" O GLY J 108 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU J 113 " --> pdb=" O ILE J 109 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE J 114 " --> pdb=" O PRO J 110 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRP J 115 " --> pdb=" O MET J 111 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA J 120 " --> pdb=" O GLY J 116 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE J 121 " --> pdb=" O ILE J 117 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU J 122 " --> pdb=" O TYR J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 129 through 141 removed outlier: 3.846A pdb=" N LEU J 138 " --> pdb=" O ILE J 134 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE J 139 " --> pdb=" O LYS J 135 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU J 140 " --> pdb=" O SER J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 156 Processing helix chain 'J' and resid 158 through 163 removed outlier: 3.564A pdb=" N ALA J 162 " --> pdb=" O PRO J 158 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL J 163 " --> pdb=" O LEU J 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 158 through 163' Processing helix chain 'J' and resid 164 through 168 removed outlier: 4.037A pdb=" N PHE J 167 " --> pdb=" O GLY J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 71 Processing helix chain 'K' and resid 81 through 107 removed outlier: 4.368A pdb=" N ALA K 87 " --> pdb=" O GLY K 83 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE K 89 " --> pdb=" O TRP K 85 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR K 90 " --> pdb=" O LYS K 86 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS K 96 " --> pdb=" O PHE K 92 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR K 100 " --> pdb=" O LYS K 96 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG K 101 " --> pdb=" O TYR K 97 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE K 107 " --> pdb=" O LEU K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 129 removed outlier: 3.704A pdb=" N ALA K 112 " --> pdb=" O GLY K 108 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU K 113 " --> pdb=" O ILE K 109 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE K 114 " --> pdb=" O PRO K 110 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP K 115 " --> pdb=" O MET K 111 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA K 120 " --> pdb=" O GLY K 116 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE K 121 " --> pdb=" O ILE K 117 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU K 122 " --> pdb=" O TYR K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 129 through 141 removed outlier: 3.846A pdb=" N LEU K 138 " --> pdb=" O ILE K 134 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE K 139 " --> pdb=" O LYS K 135 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU K 140 " --> pdb=" O SER K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 156 Processing helix chain 'K' and resid 158 through 163 removed outlier: 3.565A pdb=" N ALA K 162 " --> pdb=" O PRO K 158 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL K 163 " --> pdb=" O LEU K 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 158 through 163' Processing helix chain 'K' and resid 164 through 168 removed outlier: 4.037A pdb=" N PHE K 167 " --> pdb=" O GLY K 164 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 176 removed outlier: 3.690A pdb=" N VAL A 170 " --> pdb=" O ARG B 171 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN B 175 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 174 " --> pdb=" O GLN B 175 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL B 170 " --> pdb=" O ARG C 171 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN C 175 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 174 " --> pdb=" O GLN C 175 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL C 170 " --> pdb=" O ARG D 171 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN D 175 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU C 174 " --> pdb=" O GLN D 175 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL D 170 " --> pdb=" O ARG E 171 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN E 175 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU D 174 " --> pdb=" O GLN E 175 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL E 170 " --> pdb=" O ARG F 171 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN F 175 " --> pdb=" O ILE E 172 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU E 174 " --> pdb=" O GLN F 175 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL F 170 " --> pdb=" O ARG G 171 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN G 175 " --> pdb=" O ILE F 172 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU F 174 " --> pdb=" O GLN G 175 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL G 170 " --> pdb=" O ARG H 171 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN H 175 " --> pdb=" O ILE G 172 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU G 174 " --> pdb=" O GLN H 175 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL H 170 " --> pdb=" O ARG I 171 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN I 175 " --> pdb=" O ILE H 172 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU H 174 " --> pdb=" O GLN I 175 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL I 170 " --> pdb=" O ARG J 171 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN J 175 " --> pdb=" O ILE I 172 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU I 174 " --> pdb=" O GLN J 175 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL J 170 " --> pdb=" O ARG K 171 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN K 175 " --> pdb=" O ILE J 172 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU J 174 " --> pdb=" O GLN K 175 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ARG A 171 " --> pdb=" O VAL K 170 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ILE K 172 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN A 173 " --> pdb=" O ILE K 172 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N LEU K 174 " --> pdb=" O ASN A 173 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLN A 175 " --> pdb=" O LEU K 174 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N LYS K 176 " --> pdb=" O GLN A 175 " (cutoff:3.500A) 538 hydrogen bonds defined for protein. 1515 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 4.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3476 1.34 - 1.46: 3024 1.46 - 1.58: 5435 1.58 - 1.69: 0 1.69 - 1.81: 55 Bond restraints: 11990 Sorted by residual: bond pdb=" C ILE G 109 " pdb=" N PRO G 110 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.08e-02 8.57e+03 2.79e+00 bond pdb=" C ILE J 109 " pdb=" N PRO J 110 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.08e-02 8.57e+03 2.79e+00 bond pdb=" C ILE A 109 " pdb=" N PRO A 110 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.08e-02 8.57e+03 2.79e+00 bond pdb=" C ILE F 109 " pdb=" N PRO F 110 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.08e-02 8.57e+03 2.73e+00 bond pdb=" C ILE H 109 " pdb=" N PRO H 110 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.08e-02 8.57e+03 2.73e+00 ... (remaining 11985 not shown) Histogram of bond angle deviations from ideal: 100.97 - 107.57: 467 107.57 - 114.17: 6951 114.17 - 120.78: 5257 120.78 - 127.38: 3484 127.38 - 133.98: 176 Bond angle restraints: 16335 Sorted by residual: angle pdb=" C ASN D 53 " pdb=" N ARG D 54 " pdb=" CA ARG D 54 " ideal model delta sigma weight residual 121.54 126.21 -4.67 1.91e+00 2.74e-01 5.99e+00 angle pdb=" C ASN K 53 " pdb=" N ARG K 54 " pdb=" CA ARG K 54 " ideal model delta sigma weight residual 121.54 126.21 -4.67 1.91e+00 2.74e-01 5.98e+00 angle pdb=" C ASN A 53 " pdb=" N ARG A 54 " pdb=" CA ARG A 54 " ideal model delta sigma weight residual 121.54 126.21 -4.67 1.91e+00 2.74e-01 5.97e+00 angle pdb=" C ASN J 53 " pdb=" N ARG J 54 " pdb=" CA ARG J 54 " ideal model delta sigma weight residual 121.54 126.20 -4.66 1.91e+00 2.74e-01 5.94e+00 angle pdb=" C ASN G 53 " pdb=" N ARG G 54 " pdb=" CA ARG G 54 " ideal model delta sigma weight residual 121.54 126.19 -4.65 1.91e+00 2.74e-01 5.93e+00 ... (remaining 16330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 6578 17.70 - 35.39: 275 35.39 - 53.09: 22 53.09 - 70.79: 0 70.79 - 88.48: 11 Dihedral angle restraints: 6886 sinusoidal: 2695 harmonic: 4191 Sorted by residual: dihedral pdb=" CB GLU G 76 " pdb=" CG GLU G 76 " pdb=" CD GLU G 76 " pdb=" OE1 GLU G 76 " ideal model delta sinusoidal sigma weight residual 0.00 88.48 -88.48 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU K 76 " pdb=" CG GLU K 76 " pdb=" CD GLU K 76 " pdb=" OE1 GLU K 76 " ideal model delta sinusoidal sigma weight residual 0.00 88.48 -88.48 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU C 76 " pdb=" CG GLU C 76 " pdb=" CD GLU C 76 " pdb=" OE1 GLU C 76 " ideal model delta sinusoidal sigma weight residual 0.00 88.48 -88.48 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 6883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1444 0.046 - 0.093: 319 0.093 - 0.139: 85 0.139 - 0.185: 0 0.185 - 0.231: 11 Chirality restraints: 1859 Sorted by residual: chirality pdb=" CB ILE G 141 " pdb=" CA ILE G 141 " pdb=" CG1 ILE G 141 " pdb=" CG2 ILE G 141 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB ILE I 141 " pdb=" CA ILE I 141 " pdb=" CG1 ILE I 141 " pdb=" CG2 ILE I 141 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE B 141 " pdb=" CA ILE B 141 " pdb=" CG1 ILE B 141 " pdb=" CG2 ILE B 141 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1856 not shown) Planarity restraints: 1991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 109 " -0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO F 110 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO F 110 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 110 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 109 " 0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO A 110 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 110 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 110 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE K 109 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.58e+00 pdb=" N PRO K 110 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO K 110 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO K 110 " 0.018 5.00e-02 4.00e+02 ... (remaining 1988 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 5110 2.96 - 3.45: 10121 3.45 - 3.93: 16712 3.93 - 4.42: 17201 4.42 - 4.90: 31692 Nonbonded interactions: 80836 Sorted by model distance: nonbonded pdb=" NZ LYS A 165 " pdb=" OD1 ASP K 157 " model vdw 2.479 2.520 nonbonded pdb=" OD1 ASP B 157 " pdb=" NZ LYS C 165 " model vdw 2.483 2.520 nonbonded pdb=" OD1 ASP A 157 " pdb=" NZ LYS B 165 " model vdw 2.485 2.520 nonbonded pdb=" OD1 ASP E 157 " pdb=" NZ LYS F 165 " model vdw 2.485 2.520 nonbonded pdb=" OD1 ASP I 157 " pdb=" NZ LYS J 165 " model vdw 2.488 2.520 ... (remaining 80831 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.360 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: 0.010 Extract box with map and model: 14.280 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 29.730 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11990 Z= 0.161 Angle : 0.523 4.922 16335 Z= 0.305 Chirality : 0.043 0.231 1859 Planarity : 0.003 0.031 1991 Dihedral : 10.005 88.483 4158 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer Outliers : 0.00 % 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: -2.84 (0.20), residues: 1397 helix: -0.90 (0.16), residues: 814 sheet: None (None), residues: 0 loop : -3.37 (0.23), residues: 583 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.164 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2709 time to fit residues: 54.8532 Evaluate side-chains 129 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.293 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7723 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 11990 Z= 0.250 Angle : 0.608 5.404 16335 Z= 0.351 Chirality : 0.046 0.136 1859 Planarity : 0.004 0.030 1991 Dihedral : 4.384 16.414 1507 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer Outliers : 0.47 % 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: -1.61 (0.22), residues: 1397 helix: 0.23 (0.18), residues: 836 sheet: None (None), residues: 0 loop : -3.19 (0.25), residues: 561 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 158 time to evaluate : 1.246 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 162 average time/residue: 0.2374 time to fit residues: 55.1305 Evaluate side-chains 150 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 148 time to evaluate : 1.304 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1007 time to fit residues: 2.0548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 120 optimal weight: 0.0470 chunk 129 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 0.0970 overall best weight: 0.4876 ------------------------------------------------------------------------------- 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: 0.7663 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 11990 Z= 0.176 Angle : 0.506 4.547 16335 Z= 0.288 Chirality : 0.042 0.148 1859 Planarity : 0.003 0.026 1991 Dihedral : 4.380 16.152 1507 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.38 (0.23), residues: 1397 helix: 0.48 (0.19), residues: 836 sheet: None (None), residues: 0 loop : -3.23 (0.24), residues: 561 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 173 time to evaluate : 1.187 Fit side-chains outliers start: 27 outliers final: 21 residues processed: 189 average time/residue: 0.2702 time to fit residues: 70.1792 Evaluate side-chains 169 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 148 time to evaluate : 1.185 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1133 time to fit residues: 5.8928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 120 optimal weight: 0.0670 chunk 127 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- 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: 0.7728 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11990 Z= 0.201 Angle : 0.519 4.582 16335 Z= 0.295 Chirality : 0.042 0.155 1859 Planarity : 0.003 0.028 1991 Dihedral : 4.242 15.188 1507 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.31 % Favored : 89.62 % Rotamer Outliers : 1.55 % 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: -1.11 (0.23), residues: 1397 helix: 0.63 (0.19), residues: 847 sheet: None (None), residues: 0 loop : -3.06 (0.25), residues: 550 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 152 time to evaluate : 1.319 Fit side-chains outliers start: 20 outliers final: 14 residues processed: 156 average time/residue: 0.2674 time to fit residues: 58.1626 Evaluate side-chains 156 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1239 time to fit residues: 4.8609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.0010 chunk 1 optimal weight: 0.2980 chunk 95 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 0.0980 chunk 88 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 114 optimal weight: 0.0870 chunk 32 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 overall best weight: 0.2364 ------------------------------------------------------------------------------- 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: 0.7629 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 11990 Z= 0.147 Angle : 0.469 4.502 16335 Z= 0.264 Chirality : 0.041 0.120 1859 Planarity : 0.003 0.027 1991 Dihedral : 4.302 16.386 1507 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer Outliers : 1.09 % 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: -0.97 (0.24), residues: 1397 helix: 0.85 (0.19), residues: 836 sheet: None (None), residues: 0 loop : -3.13 (0.25), residues: 561 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 158 time to evaluate : 1.292 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 160 average time/residue: 0.2603 time to fit residues: 57.9723 Evaluate side-chains 158 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 149 time to evaluate : 1.672 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1007 time to fit residues: 3.1424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.7765 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 11990 Z= 0.226 Angle : 0.529 4.887 16335 Z= 0.301 Chirality : 0.043 0.156 1859 Planarity : 0.003 0.030 1991 Dihedral : 4.194 14.918 1507 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.09 % Favored : 89.76 % Rotamer Outliers : 0.85 % 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: -0.95 (0.24), residues: 1397 helix: 0.79 (0.19), residues: 847 sheet: None (None), residues: 0 loop : -3.06 (0.25), residues: 550 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 1.150 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 145 average time/residue: 0.2910 time to fit residues: 57.9455 Evaluate side-chains 147 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 141 time to evaluate : 1.285 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1001 time to fit residues: 2.9246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 78 optimal weight: 0.0070 chunk 50 optimal weight: 0.6980 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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: 0.7729 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11990 Z= 0.183 Angle : 0.498 4.548 16335 Z= 0.283 Chirality : 0.042 0.127 1859 Planarity : 0.003 0.029 1991 Dihedral : 4.276 15.658 1507 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.45 % Favored : 90.41 % Rotamer Outliers : 1.09 % 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: -0.96 (0.24), residues: 1397 helix: 0.91 (0.19), residues: 836 sheet: None (None), residues: 0 loop : -3.22 (0.24), residues: 561 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 150 time to evaluate : 1.346 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 151 average time/residue: 0.2701 time to fit residues: 56.6143 Evaluate side-chains 155 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 1.390 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1142 time to fit residues: 3.2961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 chunk 62 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7748 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 11990 Z= 0.196 Angle : 0.505 4.563 16335 Z= 0.287 Chirality : 0.042 0.132 1859 Planarity : 0.003 0.030 1991 Dihedral : 4.230 15.327 1507 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer Outliers : 1.09 % 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: -0.88 (0.24), residues: 1397 helix: 0.98 (0.19), residues: 836 sheet: None (None), residues: 0 loop : -3.19 (0.24), residues: 561 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 1.262 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 158 average time/residue: 0.2734 time to fit residues: 60.1331 Evaluate side-chains 161 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 154 time to evaluate : 1.259 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1049 time to fit residues: 3.1920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.9990 chunk 121 optimal weight: 0.4980 chunk 71 optimal weight: 0.0270 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 chunk 107 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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: 0.7710 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 11990 Z= 0.169 Angle : 0.489 4.529 16335 Z= 0.276 Chirality : 0.041 0.149 1859 Planarity : 0.003 0.030 1991 Dihedral : 4.264 15.543 1507 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.31 % Favored : 90.62 % Rotamer Outliers : 0.54 % 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: -0.82 (0.24), residues: 1397 helix: 1.04 (0.19), residues: 836 sheet: None (None), residues: 0 loop : -3.18 (0.25), residues: 561 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 155 time to evaluate : 1.161 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 157 average time/residue: 0.2685 time to fit residues: 58.4416 Evaluate side-chains 155 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 153 time to evaluate : 1.305 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1196 time to fit residues: 2.2654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 0.0870 chunk 121 optimal weight: 0.3980 chunk 104 optimal weight: 0.0000 chunk 10 optimal weight: 0.6980 chunk 80 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 32 optimal weight: 0.0870 overall best weight: 0.2140 ------------------------------------------------------------------------------- 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: 0.7622 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 11990 Z= 0.144 Angle : 0.464 4.531 16335 Z= 0.258 Chirality : 0.041 0.135 1859 Planarity : 0.003 0.030 1991 Dihedral : 4.229 16.060 1507 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer Outliers : 0.16 % 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: -0.64 (0.24), residues: 1397 helix: 1.06 (0.19), residues: 880 sheet: None (None), residues: 0 loop : -3.22 (0.26), residues: 517 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 165 time to evaluate : 1.294 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 165 average time/residue: 0.2699 time to fit residues: 61.7369 Evaluate side-chains 164 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 1.298 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1368 time to fit residues: 2.0493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.0170 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.163720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.142552 restraints weight = 14410.181| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.72 r_work: 0.3540 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11990 Z= 0.209 Angle : 0.508 4.636 16335 Z= 0.287 Chirality : 0.042 0.135 1859 Planarity : 0.003 0.029 1991 Dihedral : 4.157 15.364 1507 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.79 % Allowed : 9.09 % Favored : 90.12 % Rotamer Outliers : 0.47 % 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: -0.63 (0.24), residues: 1397 helix: 1.07 (0.19), residues: 880 sheet: None (None), residues: 0 loop : -3.21 (0.26), residues: 517 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2357.91 seconds wall clock time: 43 minutes 19.91 seconds (2599.91 seconds total)