Starting phenix.real_space_refine on Wed Sep 25 23:05:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc0_25007/09_2024/7sc0_25007.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc0_25007/09_2024/7sc0_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_25007/09_2024/7sc0_25007.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc0_25007/09_2024/7sc0_25007.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc0_25007/09_2024/7sc0_25007.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc0_25007/09_2024/7sc0_25007.cif" } 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. Time to flip 22 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11638 Number of models: 1 Model: "" Number of chains: 1 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} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J Time building chain proxies: 4.32, per 1000 atoms: 0.37 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 - 3.00 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: 3.01 Conformation dependent library (CDL) restraints added in 1.4 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: 1.30 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: 2.97 Time building geometry restraints manager: 3.43 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: 0.00 - 0.98: 15533 0.98 - 1.97: 608 1.97 - 2.95: 108 2.95 - 3.94: 42 3.94 - 4.92: 44 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 3.120 nonbonded pdb=" OD1 ASP B 157 " pdb=" NZ LYS C 165 " model vdw 2.483 3.120 nonbonded pdb=" OD1 ASP A 157 " pdb=" NZ LYS B 165 " model vdw 2.485 3.120 nonbonded pdb=" OD1 ASP E 157 " pdb=" NZ LYS F 165 " model vdw 2.485 3.120 nonbonded pdb=" OD1 ASP I 157 " pdb=" NZ LYS J 165 " model vdw 2.488 3.120 ... (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 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' } 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: 6.600 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 25.010 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.030 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.540 ------------------------------------------------------------------------------- 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 % Allowed : 0.00 % Favored : 100.00 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 128 HIS 0.001 0.000 HIS I 153 PHE 0.006 0.001 PHE H 137 TYR 0.004 0.001 TYR I 148 ARG 0.001 0.000 ARG H 101 *********************** 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 : 1.398 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2611 time to fit residues: 53.0627 Evaluate side-chains 129 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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: 0.6980 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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: 0.7719 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11990 Z= 0.255 Angle : 0.618 5.897 16335 Z= 0.355 Chirality : 0.047 0.145 1859 Planarity : 0.004 0.031 1991 Dihedral : 4.416 16.337 1507 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.30 % Favored : 91.05 % Rotamer: Outliers : 0.54 % Allowed : 3.89 % Favored : 95.57 % 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: -1.74 (0.22), residues: 1397 helix: 0.07 (0.18), residues: 836 sheet: None (None), residues: 0 loop : -3.17 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 128 HIS 0.004 0.001 HIS I 126 PHE 0.019 0.002 PHE H 107 TYR 0.008 0.001 TYR C 148 ARG 0.001 0.000 ARG E 146 *********************** 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 165 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 158 time to evaluate : 1.444 Fit side-chains REVERT: I 61 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7402 (m-30) outliers start: 7 outliers final: 2 residues processed: 162 average time/residue: 0.2769 time to fit residues: 63.3693 Evaluate side-chains 152 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 149 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain I residue 61 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 120 optimal weight: 0.0370 chunk 129 optimal weight: 0.0570 chunk 106 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 96 optimal weight: 0.0970 overall best weight: 0.2374 ------------------------------------------------------------------------------- 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: 0.7594 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11990 Z= 0.155 Angle : 0.490 4.433 16335 Z= 0.278 Chirality : 0.042 0.116 1859 Planarity : 0.003 0.029 1991 Dihedral : 4.361 17.015 1507 Min Nonbonded Distance : 2.676 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 2.41 % Allowed : 5.05 % Favored : 92.54 % 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: -1.31 (0.23), residues: 1397 helix: 0.53 (0.19), residues: 836 sheet: None (None), residues: 0 loop : -3.20 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 128 HIS 0.002 0.001 HIS J 126 PHE 0.010 0.001 PHE A 89 TYR 0.008 0.001 TYR I 118 ARG 0.001 0.000 ARG B 101 *********************** 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 211 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 180 time to evaluate : 1.290 Fit side-chains REVERT: B 61 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7491 (m-30) outliers start: 31 outliers final: 26 residues processed: 192 average time/residue: 0.2863 time to fit residues: 75.7163 Evaluate side-chains 179 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 152 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 175 GLN Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 175 GLN Chi-restraints excluded: chain G residue 175 GLN Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain H residue 175 GLN Chi-restraints excluded: chain I residue 69 GLU Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 175 GLN Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 175 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 1.9990 chunk 90 optimal weight: 0.0000 chunk 62 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 127 optimal weight: 0.4980 chunk 114 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- 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: 0.7648 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11990 Z= 0.168 Angle : 0.490 4.612 16335 Z= 0.276 Chirality : 0.041 0.122 1859 Planarity : 0.003 0.031 1991 Dihedral : 4.151 15.348 1507 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 1.32 % Allowed : 7.30 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.02 (0.23), residues: 1397 helix: 0.70 (0.19), residues: 847 sheet: None (None), residues: 0 loop : -3.02 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 128 HIS 0.002 0.000 HIS J 126 PHE 0.011 0.001 PHE C 137 TYR 0.005 0.001 TYR H 148 ARG 0.001 0.000 ARG B 101 *********************** 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 164 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 1.344 Fit side-chains REVERT: B 61 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7522 (m-30) REVERT: I 61 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7430 (m-30) outliers start: 17 outliers final: 8 residues processed: 152 average time/residue: 0.2698 time to fit residues: 56.9680 Evaluate side-chains 151 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 141 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 175 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.3980 chunk 1 optimal weight: 3.9990 chunk 95 optimal weight: 0.2980 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 0.3980 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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: 0.7677 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11990 Z= 0.170 Angle : 0.491 4.533 16335 Z= 0.277 Chirality : 0.042 0.124 1859 Planarity : 0.003 0.032 1991 Dihedral : 4.160 15.208 1507 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 2.49 % Allowed : 6.68 % Favored : 90.83 % 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: -0.92 (0.24), residues: 1397 helix: 0.90 (0.19), residues: 836 sheet: None (None), residues: 0 loop : -3.11 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 115 HIS 0.002 0.000 HIS J 126 PHE 0.011 0.001 PHE C 137 TYR 0.006 0.001 TYR A 118 ARG 0.001 0.000 ARG B 101 *********************** 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 174 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 142 time to evaluate : 1.351 Fit side-chains REVERT: B 61 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7533 (t0) REVERT: I 61 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7462 (m-30) outliers start: 32 outliers final: 22 residues processed: 156 average time/residue: 0.2608 time to fit residues: 56.5200 Evaluate side-chains 162 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 154 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.9990 chunk 25 optimal weight: 0.0270 chunk 74 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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: 0.7692 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11990 Z= 0.179 Angle : 0.492 4.770 16335 Z= 0.278 Chirality : 0.042 0.125 1859 Planarity : 0.003 0.032 1991 Dihedral : 4.124 15.119 1507 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 2.95 % Allowed : 6.53 % Favored : 90.52 % 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: 0.86 (0.19), residues: 847 sheet: None (None), residues: 0 loop : -3.06 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP D 98 HIS 0.002 0.000 HIS J 126 PHE 0.011 0.001 PHE C 137 TYR 0.006 0.001 TYR J 148 ARG 0.009 0.000 ARG K 101 *********************** 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 184 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 146 time to evaluate : 1.328 Fit side-chains REVERT: B 61 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7570 (t0) REVERT: C 49 ILE cc_start: 0.7423 (mm) cc_final: 0.6793 (mm) REVERT: E 61 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7617 (m-30) REVERT: I 61 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7459 (m-30) outliers start: 38 outliers final: 28 residues processed: 154 average time/residue: 0.2656 time to fit residues: 56.6735 Evaluate side-chains 176 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 145 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 69 GLU Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 154 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.7980 chunk 72 optimal weight: 0.0010 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 127 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 50 optimal weight: 0.1980 overall best weight: 0.4186 ------------------------------------------------------------------------------- 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: 0.7671 moved from start: 0.3607 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= 0.162 Angle : 0.480 4.505 16335 Z= 0.270 Chirality : 0.041 0.123 1859 Planarity : 0.003 0.031 1991 Dihedral : 4.155 15.280 1507 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 0.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 2.95 % Allowed : 6.76 % Favored : 90.29 % 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: -0.85 (0.24), residues: 1397 helix: 1.00 (0.19), residues: 836 sheet: None (None), residues: 0 loop : -3.17 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP D 98 HIS 0.002 0.000 HIS H 126 PHE 0.012 0.001 PHE J 81 TYR 0.005 0.001 TYR K 100 ARG 0.001 0.000 ARG K 101 *********************** 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 190 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 152 time to evaluate : 1.290 Fit side-chains REVERT: B 61 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7659 (t0) REVERT: C 49 ILE cc_start: 0.7470 (mm) cc_final: 0.6811 (mm) REVERT: E 61 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7627 (m-30) REVERT: I 61 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7494 (m-30) outliers start: 38 outliers final: 28 residues processed: 155 average time/residue: 0.2641 time to fit residues: 57.5532 Evaluate side-chains 181 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 150 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 69 GLU Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain K residue 59 LEU Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 154 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 80 optimal weight: 0.0570 chunk 86 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 0.0670 chunk 100 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- 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: 0.7679 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11990 Z= 0.167 Angle : 0.480 4.494 16335 Z= 0.270 Chirality : 0.041 0.125 1859 Planarity : 0.003 0.030 1991 Dihedral : 4.100 15.257 1507 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 2.33 % Allowed : 7.23 % Favored : 90.44 % 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: -0.78 (0.24), residues: 1397 helix: 0.95 (0.19), residues: 880 sheet: None (None), residues: 0 loop : -3.28 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP C 98 HIS 0.002 0.000 HIS J 126 PHE 0.012 0.001 PHE J 81 TYR 0.005 0.001 TYR K 100 ARG 0.001 0.000 ARG K 101 *********************** 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 190 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 160 time to evaluate : 1.351 Fit side-chains REVERT: B 61 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7690 (t0) REVERT: E 61 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7639 (m-30) REVERT: G 49 ILE cc_start: 0.7424 (mm) cc_final: 0.6746 (mm) REVERT: I 61 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7481 (m-30) outliers start: 30 outliers final: 22 residues processed: 164 average time/residue: 0.2480 time to fit residues: 56.6869 Evaluate side-chains 181 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 156 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 69 GLU Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 154 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 0.2980 chunk 36 optimal weight: 0.0050 chunk 107 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 125 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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: 0.7690 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11990 Z= 0.168 Angle : 0.486 4.505 16335 Z= 0.273 Chirality : 0.042 0.126 1859 Planarity : 0.003 0.030 1991 Dihedral : 4.123 15.231 1507 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 2.49 % Allowed : 7.54 % Favored : 89.98 % 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: -0.76 (0.24), residues: 1397 helix: 0.97 (0.19), residues: 880 sheet: None (None), residues: 0 loop : -3.27 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 98 HIS 0.002 0.000 HIS J 126 PHE 0.013 0.001 PHE J 81 TYR 0.010 0.001 TYR J 97 ARG 0.001 0.000 ARG K 101 *********************** 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 196 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 164 time to evaluate : 1.298 Fit side-chains REVERT: E 61 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7615 (m-30) REVERT: G 49 ILE cc_start: 0.7463 (mm) cc_final: 0.6799 (mm) REVERT: H 49 ILE cc_start: 0.7583 (mm) cc_final: 0.7131 (mm) REVERT: I 61 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7467 (m-30) outliers start: 32 outliers final: 24 residues processed: 168 average time/residue: 0.2480 time to fit residues: 58.4382 Evaluate side-chains 190 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 69 GLU Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 154 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.0370 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 104 optimal weight: 0.0020 chunk 10 optimal weight: 0.6980 chunk 80 optimal weight: 0.0980 chunk 64 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.2866 ------------------------------------------------------------------------------- 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: 0.7640 moved from start: 0.3904 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= 0.148 Angle : 0.468 4.482 16335 Z= 0.261 Chirality : 0.041 0.129 1859 Planarity : 0.003 0.030 1991 Dihedral : 4.099 15.570 1507 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 1.63 % Allowed : 8.39 % Favored : 89.98 % 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: -0.66 (0.24), residues: 1397 helix: 1.04 (0.19), residues: 880 sheet: None (None), residues: 0 loop : -3.23 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 98 HIS 0.002 0.000 HIS H 126 PHE 0.012 0.001 PHE H 107 TYR 0.009 0.001 TYR J 97 ARG 0.002 0.000 ARG K 101 ********************** 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 195 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 174 time to evaluate : 1.301 Fit side-chains REVERT: H 49 ILE cc_start: 0.7619 (mm) cc_final: 0.7204 (mm) REVERT: I 61 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7484 (m-30) outliers start: 21 outliers final: 19 residues processed: 174 average time/residue: 0.2550 time to fit residues: 61.6596 Evaluate side-chains 189 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 169 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 69 GLU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain K residue 61 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.160099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.139681 restraints weight = 14146.489| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.62 r_work: 0.3539 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11990 Z= 0.224 Angle : 0.525 4.591 16335 Z= 0.298 Chirality : 0.043 0.158 1859 Planarity : 0.003 0.028 1991 Dihedral : 4.112 15.306 1507 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.79 % Allowed : 9.16 % Favored : 90.05 % Rotamer: Outliers : 2.18 % Allowed : 8.16 % Favored : 89.67 % 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: -0.76 (0.24), residues: 1397 helix: 1.09 (0.19), residues: 836 sheet: None (None), residues: 0 loop : -3.17 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 98 HIS 0.002 0.001 HIS J 126 PHE 0.017 0.002 PHE J 81 TYR 0.010 0.001 TYR F 97 ARG 0.001 0.000 ARG K 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2472.83 seconds wall clock time: 45 minutes 2.80 seconds (2702.80 seconds total)