Starting phenix.real_space_refine on Wed Nov 20 13:48:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7g_4740/11_2024/6r7g_4740.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7g_4740/11_2024/6r7g_4740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7g_4740/11_2024/6r7g_4740.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7g_4740/11_2024/6r7g_4740.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7g_4740/11_2024/6r7g_4740.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7g_4740/11_2024/6r7g_4740.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 69 5.49 5 S 130 5.16 5 C 13595 2.51 5 N 3687 2.21 5 O 4531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 22012 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1580 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 14, 'TRANS': 194} Chain: "R" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1380 Classifications: {'RNA': 69} Modifications used: {'rna2p_pyr': 13, 'rna3p_pyr': 56} Link IDs: {'rna2p': 13, 'rna3p': 55} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M Time building chain proxies: 7.68, per 1000 atoms: 0.35 Number of scatterers: 22012 At special positions: 0 Unit cell: (139.763, 141.417, 109.991, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 130 16.00 P 69 15.00 O 4531 8.00 N 3687 7.00 C 13595 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: 4.02 Conformation dependent library (CDL) restraints added in 2.5 seconds 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5174 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 0 sheets defined 59.8% alpha, 0.0% beta 0 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 5.87 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR A 34 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 72 through 74 No H-bonds generated for 'chain 'A' and resid 72 through 74' Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.618A pdb=" N ASP A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 118 Processing helix chain 'A' and resid 122 through 130 removed outlier: 3.762A pdb=" N TYR A 130 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 154 through 161 removed outlier: 3.533A pdb=" N LYS A 158 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE A 159 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 removed outlier: 4.053A pdb=" N THR A 169 " --> pdb=" O ASN A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 206 Processing helix chain 'A' and resid 214 through 219 Processing helix chain 'A' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL A 231 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR B 34 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 55 through 69 Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 75 through 90 removed outlier: 3.619A pdb=" N ASP B 89 " --> pdb=" O ARG B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 118 Processing helix chain 'B' and resid 122 through 130 removed outlier: 3.762A pdb=" N TYR B 130 " --> pdb=" O PHE B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 154 through 161 removed outlier: 3.533A pdb=" N LYS B 158 " --> pdb=" O PRO B 155 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE B 159 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 removed outlier: 4.053A pdb=" N THR B 169 " --> pdb=" O ASN B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 206 Processing helix chain 'B' and resid 214 through 219 Processing helix chain 'B' and resid 227 through 231 removed outlier: 3.623A pdb=" N VAL B 231 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 34 removed outlier: 3.661A pdb=" N THR C 34 " --> pdb=" O GLY C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 Processing helix chain 'C' and resid 55 through 69 Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 75 through 90 removed outlier: 3.619A pdb=" N ASP C 89 " --> pdb=" O ARG C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 118 Processing helix chain 'C' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR C 130 " --> pdb=" O PHE C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 142 Processing helix chain 'C' and resid 154 through 161 removed outlier: 3.532A pdb=" N LYS C 158 " --> pdb=" O PRO C 155 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE C 159 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 removed outlier: 4.054A pdb=" N THR C 169 " --> pdb=" O ASN C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 206 Processing helix chain 'C' and resid 214 through 219 Processing helix chain 'C' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL C 231 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR D 34 " --> pdb=" O GLY D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 44 Processing helix chain 'D' and resid 55 through 69 Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 75 through 90 removed outlier: 3.618A pdb=" N ASP D 89 " --> pdb=" O ARG D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 118 Processing helix chain 'D' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR D 130 " --> pdb=" O PHE D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 142 Processing helix chain 'D' and resid 154 through 161 removed outlier: 3.532A pdb=" N LYS D 158 " --> pdb=" O PRO D 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE D 159 " --> pdb=" O GLU D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 169 removed outlier: 4.053A pdb=" N THR D 169 " --> pdb=" O ASN D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 206 Processing helix chain 'D' and resid 214 through 219 Processing helix chain 'D' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL D 231 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 34 removed outlier: 3.659A pdb=" N THR E 34 " --> pdb=" O GLY E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 44 Processing helix chain 'E' and resid 55 through 69 Processing helix chain 'E' and resid 72 through 74 No H-bonds generated for 'chain 'E' and resid 72 through 74' Processing helix chain 'E' and resid 75 through 90 removed outlier: 3.618A pdb=" N ASP E 89 " --> pdb=" O ARG E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 118 Processing helix chain 'E' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR E 130 " --> pdb=" O PHE E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 154 through 161 removed outlier: 3.532A pdb=" N LYS E 158 " --> pdb=" O PRO E 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE E 159 " --> pdb=" O GLU E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 169 removed outlier: 4.052A pdb=" N THR E 169 " --> pdb=" O ASN E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 206 Processing helix chain 'E' and resid 214 through 219 Processing helix chain 'E' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL E 231 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR F 34 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 44 Processing helix chain 'F' and resid 55 through 69 Processing helix chain 'F' and resid 72 through 74 No H-bonds generated for 'chain 'F' and resid 72 through 74' Processing helix chain 'F' and resid 75 through 90 removed outlier: 3.619A pdb=" N ASP F 89 " --> pdb=" O ARG F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 118 Processing helix chain 'F' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR F 130 " --> pdb=" O PHE F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 142 Processing helix chain 'F' and resid 154 through 161 removed outlier: 3.533A pdb=" N LYS F 158 " --> pdb=" O PRO F 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE F 159 " --> pdb=" O GLU F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 169 removed outlier: 4.053A pdb=" N THR F 169 " --> pdb=" O ASN F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 206 Processing helix chain 'F' and resid 214 through 219 Processing helix chain 'F' and resid 227 through 231 removed outlier: 3.621A pdb=" N VAL F 231 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 34 removed outlier: 3.661A pdb=" N THR G 34 " --> pdb=" O GLY G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 44 Processing helix chain 'G' and resid 55 through 69 Processing helix chain 'G' and resid 72 through 74 No H-bonds generated for 'chain 'G' and resid 72 through 74' Processing helix chain 'G' and resid 75 through 90 removed outlier: 3.618A pdb=" N ASP G 89 " --> pdb=" O ARG G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 118 Processing helix chain 'G' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR G 130 " --> pdb=" O PHE G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 142 Processing helix chain 'G' and resid 154 through 161 removed outlier: 3.533A pdb=" N LYS G 158 " --> pdb=" O PRO G 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE G 159 " --> pdb=" O GLU G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 169 removed outlier: 4.052A pdb=" N THR G 169 " --> pdb=" O ASN G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 206 Processing helix chain 'G' and resid 214 through 219 Processing helix chain 'G' and resid 227 through 231 removed outlier: 3.623A pdb=" N VAL G 231 " --> pdb=" O ALA G 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR H 34 " --> pdb=" O GLY H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 44 Processing helix chain 'H' and resid 55 through 69 Processing helix chain 'H' and resid 72 through 74 No H-bonds generated for 'chain 'H' and resid 72 through 74' Processing helix chain 'H' and resid 75 through 90 removed outlier: 3.618A pdb=" N ASP H 89 " --> pdb=" O ARG H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 118 Processing helix chain 'H' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR H 130 " --> pdb=" O PHE H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 142 Processing helix chain 'H' and resid 154 through 161 removed outlier: 3.532A pdb=" N LYS H 158 " --> pdb=" O PRO H 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE H 159 " --> pdb=" O GLU H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 169 removed outlier: 4.052A pdb=" N THR H 169 " --> pdb=" O ASN H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 206 Processing helix chain 'H' and resid 214 through 219 Processing helix chain 'H' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL H 231 " --> pdb=" O ALA H 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR I 34 " --> pdb=" O GLY I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 44 Processing helix chain 'I' and resid 55 through 69 Processing helix chain 'I' and resid 72 through 74 No H-bonds generated for 'chain 'I' and resid 72 through 74' Processing helix chain 'I' and resid 75 through 90 removed outlier: 3.619A pdb=" N ASP I 89 " --> pdb=" O ARG I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 118 Processing helix chain 'I' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR I 130 " --> pdb=" O PHE I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 Processing helix chain 'I' and resid 154 through 161 removed outlier: 3.533A pdb=" N LYS I 158 " --> pdb=" O PRO I 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE I 159 " --> pdb=" O GLU I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 169 removed outlier: 4.053A pdb=" N THR I 169 " --> pdb=" O ASN I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 206 Processing helix chain 'I' and resid 214 through 219 Processing helix chain 'I' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL I 231 " --> pdb=" O ALA I 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR J 34 " --> pdb=" O GLY J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 44 Processing helix chain 'J' and resid 55 through 69 Processing helix chain 'J' and resid 72 through 74 No H-bonds generated for 'chain 'J' and resid 72 through 74' Processing helix chain 'J' and resid 75 through 90 removed outlier: 3.618A pdb=" N ASP J 89 " --> pdb=" O ARG J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 118 Processing helix chain 'J' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR J 130 " --> pdb=" O PHE J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 142 Processing helix chain 'J' and resid 154 through 161 removed outlier: 3.532A pdb=" N LYS J 158 " --> pdb=" O PRO J 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE J 159 " --> pdb=" O GLU J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 169 removed outlier: 4.053A pdb=" N THR J 169 " --> pdb=" O ASN J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 206 Processing helix chain 'J' and resid 214 through 219 Processing helix chain 'J' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL J 231 " --> pdb=" O ALA J 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR K 34 " --> pdb=" O GLY K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 44 Processing helix chain 'K' and resid 55 through 69 Processing helix chain 'K' and resid 72 through 74 No H-bonds generated for 'chain 'K' and resid 72 through 74' Processing helix chain 'K' and resid 75 through 90 removed outlier: 3.618A pdb=" N ASP K 89 " --> pdb=" O ARG K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 118 Processing helix chain 'K' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR K 130 " --> pdb=" O PHE K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 142 Processing helix chain 'K' and resid 154 through 161 removed outlier: 3.532A pdb=" N LYS K 158 " --> pdb=" O PRO K 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE K 159 " --> pdb=" O GLU K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 169 removed outlier: 4.052A pdb=" N THR K 169 " --> pdb=" O ASN K 166 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 206 Processing helix chain 'K' and resid 214 through 219 Processing helix chain 'K' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL K 231 " --> pdb=" O ALA K 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR L 34 " --> pdb=" O GLY L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 44 Processing helix chain 'L' and resid 55 through 69 Processing helix chain 'L' and resid 72 through 74 No H-bonds generated for 'chain 'L' and resid 72 through 74' Processing helix chain 'L' and resid 75 through 90 removed outlier: 3.619A pdb=" N ASP L 89 " --> pdb=" O ARG L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 118 Processing helix chain 'L' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR L 130 " --> pdb=" O PHE L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 142 Processing helix chain 'L' and resid 154 through 161 removed outlier: 3.532A pdb=" N LYS L 158 " --> pdb=" O PRO L 155 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE L 159 " --> pdb=" O GLU L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 169 removed outlier: 4.053A pdb=" N THR L 169 " --> pdb=" O ASN L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 206 Processing helix chain 'L' and resid 214 through 219 Processing helix chain 'L' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL L 231 " --> pdb=" O ALA L 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR M 34 " --> pdb=" O GLY M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 44 Processing helix chain 'M' and resid 55 through 69 Processing helix chain 'M' and resid 72 through 74 No H-bonds generated for 'chain 'M' and resid 72 through 74' Processing helix chain 'M' and resid 75 through 90 removed outlier: 3.619A pdb=" N ASP M 89 " --> pdb=" O ARG M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 118 Processing helix chain 'M' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR M 130 " --> pdb=" O PHE M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 142 Processing helix chain 'M' and resid 154 through 161 removed outlier: 3.532A pdb=" N LYS M 158 " --> pdb=" O PRO M 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE M 159 " --> pdb=" O GLU M 156 " (cutoff:3.500A) Processing helix chain 'M' and resid 164 through 169 removed outlier: 4.053A pdb=" N THR M 169 " --> pdb=" O ASN M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 206 Processing helix chain 'M' and resid 214 through 219 Processing helix chain 'M' and resid 227 through 231 removed outlier: 3.623A pdb=" N VAL M 231 " --> pdb=" O ALA M 228 " (cutoff:3.500A) 923 hydrogen bonds defined for protein. 2496 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 5.70 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5279 1.33 - 1.45: 4789 1.45 - 1.57: 12112 1.57 - 1.69: 150 1.69 - 1.81: 221 Bond restraints: 22551 Sorted by residual: bond pdb=" CA PHE F 164 " pdb=" CB PHE F 164 " ideal model delta sigma weight residual 1.532 1.566 -0.034 1.51e-02 4.39e+03 5.07e+00 bond pdb=" CA PHE K 164 " pdb=" CB PHE K 164 " ideal model delta sigma weight residual 1.532 1.566 -0.034 1.51e-02 4.39e+03 5.05e+00 bond pdb=" CA PHE M 164 " pdb=" CB PHE M 164 " ideal model delta sigma weight residual 1.532 1.566 -0.034 1.51e-02 4.39e+03 4.97e+00 bond pdb=" CA PHE C 164 " pdb=" CB PHE C 164 " ideal model delta sigma weight residual 1.532 1.566 -0.034 1.51e-02 4.39e+03 4.94e+00 bond pdb=" CA PHE I 164 " pdb=" CB PHE I 164 " ideal model delta sigma weight residual 1.532 1.565 -0.033 1.51e-02 4.39e+03 4.91e+00 ... (remaining 22546 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 28498 1.40 - 2.79: 2096 2.79 - 4.19: 354 4.19 - 5.58: 46 5.58 - 6.98: 39 Bond angle restraints: 31033 Sorted by residual: angle pdb=" CA PHE B 164 " pdb=" CB PHE B 164 " pdb=" CG PHE B 164 " ideal model delta sigma weight residual 113.80 117.11 -3.31 1.00e+00 1.00e+00 1.10e+01 angle pdb=" CA PHE J 164 " pdb=" CB PHE J 164 " pdb=" CG PHE J 164 " ideal model delta sigma weight residual 113.80 117.11 -3.31 1.00e+00 1.00e+00 1.09e+01 angle pdb=" CA PHE H 164 " pdb=" CB PHE H 164 " pdb=" CG PHE H 164 " ideal model delta sigma weight residual 113.80 117.09 -3.29 1.00e+00 1.00e+00 1.08e+01 angle pdb=" CA PHE I 164 " pdb=" CB PHE I 164 " pdb=" CG PHE I 164 " ideal model delta sigma weight residual 113.80 117.09 -3.29 1.00e+00 1.00e+00 1.08e+01 angle pdb=" CA PHE C 164 " pdb=" CB PHE C 164 " pdb=" CG PHE C 164 " ideal model delta sigma weight residual 113.80 117.08 -3.28 1.00e+00 1.00e+00 1.07e+01 ... (remaining 31028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 13406 35.52 - 71.04: 356 71.04 - 106.56: 0 106.56 - 142.08: 0 142.08 - 177.61: 1 Dihedral angle restraints: 13763 sinusoidal: 5859 harmonic: 7904 Sorted by residual: dihedral pdb=" O4' U R 29 " pdb=" C1' U R 29 " pdb=" N1 U R 29 " pdb=" C2 U R 29 " ideal model delta sinusoidal sigma weight residual -128.00 49.61 -177.61 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA ASP C 209 " pdb=" C ASP C 209 " pdb=" N PHE C 210 " pdb=" CA PHE C 210 " ideal model delta harmonic sigma weight residual 180.00 -156.60 -23.40 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA ASP H 209 " pdb=" C ASP H 209 " pdb=" N PHE H 210 " pdb=" CA PHE H 210 " ideal model delta harmonic sigma weight residual -180.00 -156.64 -23.36 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 13760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2094 0.038 - 0.077: 950 0.077 - 0.115: 394 0.115 - 0.154: 117 0.154 - 0.192: 40 Chirality restraints: 3595 Sorted by residual: chirality pdb=" CA PHE D 164 " pdb=" N PHE D 164 " pdb=" C PHE D 164 " pdb=" CB PHE D 164 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" CA PHE E 164 " pdb=" N PHE E 164 " pdb=" C PHE E 164 " pdb=" CB PHE E 164 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CA PHE A 164 " pdb=" N PHE A 164 " pdb=" C PHE A 164 " pdb=" CB PHE A 164 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.04e-01 ... (remaining 3592 not shown) Planarity restraints: 3826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 162 " 0.013 2.00e-02 2.50e+03 2.04e-02 7.26e+00 pdb=" CG PHE B 162 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE B 162 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 162 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE B 162 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 162 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 162 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE L 162 " 0.013 2.00e-02 2.50e+03 2.03e-02 7.24e+00 pdb=" CG PHE L 162 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE L 162 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE L 162 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE L 162 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE L 162 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE L 162 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.013 2.00e-02 2.50e+03 2.03e-02 7.24e+00 pdb=" CG PHE A 162 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.000 2.00e-02 2.50e+03 ... (remaining 3823 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 30 2.48 - 3.09: 14744 3.09 - 3.69: 35603 3.69 - 4.30: 54259 4.30 - 4.90: 81154 Nonbonded interactions: 185790 Sorted by model distance: nonbonded pdb=" O2 U R 65 " pdb=" O HOH R 101 " model vdw 1.880 3.040 nonbonded pdb=" OP2 U R 24 " pdb=" O HOH R 102 " model vdw 1.942 3.040 nonbonded pdb=" O2 U R 55 " pdb=" O HOH R 103 " model vdw 2.054 3.040 nonbonded pdb=" O2 U R 5 " pdb=" O HOH R 104 " model vdw 2.065 3.040 nonbonded pdb=" OP1 U R 23 " pdb=" O HOH R 105 " model vdw 2.094 3.040 ... (remaining 185785 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 40.280 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:13.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 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 : 0.006 0.055 22551 Z= 0.414 Angle : 0.850 6.978 31033 Z= 0.490 Chirality : 0.054 0.192 3595 Planarity : 0.006 0.037 3826 Dihedral : 14.935 177.605 8589 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.05 % Allowed : 3.05 % Favored : 93.90 % 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: -2.46 (0.13), residues: 2691 helix: -2.64 (0.09), residues: 1430 sheet: None (None), residues: 0 loop : -0.10 (0.16), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 135 HIS 0.003 0.001 HIS B 86 PHE 0.046 0.005 PHE L 162 TYR 0.013 0.003 TYR E 130 ARG 0.006 0.001 ARG G 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 492 time to evaluate : 2.369 Fit side-chains REVERT: A 58 ASP cc_start: 0.7589 (m-30) cc_final: 0.7267 (m-30) REVERT: A 89 ASP cc_start: 0.8312 (m-30) cc_final: 0.8100 (m-30) REVERT: A 128 MET cc_start: 0.9149 (mmm) cc_final: 0.8802 (mmm) REVERT: A 177 LYS cc_start: 0.7827 (tttm) cc_final: 0.7364 (mppt) REVERT: B 69 MET cc_start: 0.7546 (ptm) cc_final: 0.7224 (ptm) REVERT: B 138 MET cc_start: 0.8514 (mtm) cc_final: 0.8288 (mtm) REVERT: C 104 TYR cc_start: 0.8253 (m-80) cc_final: 0.7973 (m-80) REVERT: D 156 GLU cc_start: 0.8239 (pm20) cc_final: 0.8018 (pm20) REVERT: F 63 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7268 (mt-10) REVERT: F 78 GLN cc_start: 0.8572 (mp10) cc_final: 0.8307 (mp10) REVERT: G 156 GLU cc_start: 0.8278 (pm20) cc_final: 0.8070 (pm20) REVERT: I 128 MET cc_start: 0.9205 (mmm) cc_final: 0.8861 (mmm) REVERT: J 175 MET cc_start: 0.8232 (tpp) cc_final: 0.8023 (tpp) REVERT: K 69 MET cc_start: 0.8038 (ptm) cc_final: 0.7826 (ptm) REVERT: L 76 MET cc_start: 0.7855 (tpp) cc_final: 0.7442 (tpp) REVERT: L 104 TYR cc_start: 0.8221 (m-80) cc_final: 0.7829 (m-80) REVERT: M 33 PHE cc_start: 0.8525 (m-80) cc_final: 0.8232 (m-80) REVERT: M 128 MET cc_start: 0.9096 (mmm) cc_final: 0.8718 (mmm) REVERT: M 141 ASN cc_start: 0.8501 (m-40) cc_final: 0.8301 (m110) outliers start: 65 outliers final: 6 residues processed: 536 average time/residue: 1.7557 time to fit residues: 1040.7470 Evaluate side-chains 410 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 404 time to evaluate : 2.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 74 ASP Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain L residue 42 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 9.9990 chunk 201 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 68 optimal weight: 0.0170 chunk 135 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 208 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 241 optimal weight: 8.9990 overall best weight: 2.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN B 166 ASN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 ASN D 149 GLN D 166 ASN ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 ASN F 95 GLN ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 ASN ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 ASN G 206 GLN ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 ASN ** I 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 166 ASN J 95 GLN ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 166 ASN K 95 GLN ** K 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 166 ASN K 206 GLN L 95 GLN ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 ASN M 95 GLN M 166 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22551 Z= 0.232 Angle : 0.605 5.045 31033 Z= 0.336 Chirality : 0.045 0.163 3595 Planarity : 0.005 0.029 3826 Dihedral : 12.445 177.979 3955 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.17 % Allowed : 7.18 % Favored : 91.65 % 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: 0.21 (0.15), residues: 2691 helix: 0.05 (0.13), residues: 1443 sheet: None (None), residues: 0 loop : 0.50 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 135 HIS 0.003 0.001 HIS I 86 PHE 0.029 0.003 PHE H 164 TYR 0.016 0.002 TYR F 130 ARG 0.007 0.001 ARG K 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 426 time to evaluate : 2.334 Fit side-chains REVERT: A 58 ASP cc_start: 0.7507 (m-30) cc_final: 0.7198 (m-30) REVERT: A 89 ASP cc_start: 0.8398 (m-30) cc_final: 0.8051 (m-30) REVERT: A 128 MET cc_start: 0.9231 (mmm) cc_final: 0.8881 (mmm) REVERT: A 177 LYS cc_start: 0.7940 (tttm) cc_final: 0.7473 (mppt) REVERT: B 69 MET cc_start: 0.7319 (ptm) cc_final: 0.7015 (ptm) REVERT: C 199 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8492 (mttm) REVERT: D 199 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8305 (mttm) REVERT: E 35 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8098 (mp) REVERT: H 76 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7563 (ttm) REVERT: I 128 MET cc_start: 0.9271 (mmm) cc_final: 0.8907 (mmm) REVERT: J 45 ARG cc_start: 0.7501 (mmt-90) cc_final: 0.7287 (tpt170) REVERT: J 175 MET cc_start: 0.8297 (tpp) cc_final: 0.7986 (tpp) REVERT: L 104 TYR cc_start: 0.8276 (m-80) cc_final: 0.7878 (m-80) REVERT: M 33 PHE cc_start: 0.8540 (m-80) cc_final: 0.8275 (m-80) outliers start: 25 outliers final: 9 residues processed: 434 average time/residue: 2.0398 time to fit residues: 966.0000 Evaluate side-chains 421 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 408 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 69 MET Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 128 MET Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 201 optimal weight: 7.9990 chunk 164 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 241 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 239 optimal weight: 10.0000 chunk 82 optimal weight: 0.5980 chunk 194 optimal weight: 2.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 GLN ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** I 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN ** K 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 GLN ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22551 Z= 0.197 Angle : 0.543 5.049 31033 Z= 0.300 Chirality : 0.043 0.152 3595 Planarity : 0.004 0.030 3826 Dihedral : 12.195 176.793 3948 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.80 % Allowed : 8.21 % Favored : 90.99 % 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: 1.01 (0.16), residues: 2691 helix: 0.84 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.68 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 135 HIS 0.002 0.000 HIS B 86 PHE 0.029 0.002 PHE H 164 TYR 0.013 0.002 TYR F 130 ARG 0.005 0.000 ARG K 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 429 time to evaluate : 2.195 Fit side-chains REVERT: A 58 ASP cc_start: 0.7389 (m-30) cc_final: 0.7107 (m-30) REVERT: A 89 ASP cc_start: 0.8364 (m-30) cc_final: 0.8017 (m-30) REVERT: A 128 MET cc_start: 0.9227 (mmm) cc_final: 0.8934 (mmm) REVERT: A 177 LYS cc_start: 0.7969 (tttm) cc_final: 0.7497 (mppt) REVERT: B 58 ASP cc_start: 0.7627 (m-30) cc_final: 0.7297 (m-30) REVERT: B 199 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8557 (mttp) REVERT: D 199 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8258 (mttm) REVERT: E 35 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8057 (mp) REVERT: E 58 ASP cc_start: 0.7828 (m-30) cc_final: 0.7463 (m-30) REVERT: H 76 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7638 (ttm) REVERT: I 128 MET cc_start: 0.9266 (mmm) cc_final: 0.8956 (mmm) REVERT: J 35 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8065 (mp) REVERT: J 175 MET cc_start: 0.8316 (tpp) cc_final: 0.7999 (tpp) REVERT: K 76 MET cc_start: 0.7604 (tpp) cc_final: 0.7361 (ttm) REVERT: L 65 ILE cc_start: 0.8885 (mt) cc_final: 0.8651 (mt) REVERT: L 178 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6766 (mm-30) outliers start: 17 outliers final: 7 residues processed: 437 average time/residue: 2.1115 time to fit residues: 1005.8444 Evaluate side-chains 431 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 419 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain J residue 35 ILE Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 69 MET Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 9.9990 chunk 181 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 162 optimal weight: 0.5980 chunk 242 optimal weight: 0.9980 chunk 257 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 230 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 GLN ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** I 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN ** K 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 GLN ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22551 Z= 0.232 Angle : 0.578 5.076 31033 Z= 0.319 Chirality : 0.045 0.162 3595 Planarity : 0.004 0.029 3826 Dihedral : 12.268 176.998 3948 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.84 % Allowed : 8.77 % Favored : 90.38 % 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: 1.29 (0.16), residues: 2691 helix: 1.07 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.80 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 135 HIS 0.002 0.001 HIS B 86 PHE 0.030 0.003 PHE H 164 TYR 0.014 0.002 TYR F 130 ARG 0.006 0.001 ARG I 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 425 time to evaluate : 2.870 Fit side-chains REVERT: A 58 ASP cc_start: 0.7416 (m-30) cc_final: 0.7054 (m-30) REVERT: A 89 ASP cc_start: 0.8392 (m-30) cc_final: 0.8067 (m-30) REVERT: A 128 MET cc_start: 0.9254 (mmm) cc_final: 0.8940 (mmm) REVERT: A 177 LYS cc_start: 0.7971 (tttm) cc_final: 0.7530 (mppt) REVERT: B 58 ASP cc_start: 0.7627 (m-30) cc_final: 0.7335 (m-30) REVERT: B 199 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8582 (mttp) REVERT: C 30 SER cc_start: 0.7940 (p) cc_final: 0.7715 (t) REVERT: D 199 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8280 (mttm) REVERT: E 35 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8078 (mp) REVERT: E 58 ASP cc_start: 0.7814 (m-30) cc_final: 0.7443 (m-30) REVERT: F 78 GLN cc_start: 0.8511 (mp10) cc_final: 0.8264 (mp10) REVERT: H 76 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7631 (ttm) REVERT: I 128 MET cc_start: 0.9286 (mmm) cc_final: 0.8969 (mmm) REVERT: J 175 MET cc_start: 0.8336 (tpp) cc_final: 0.8014 (tpp) REVERT: L 65 ILE cc_start: 0.8890 (mt) cc_final: 0.8636 (mt) outliers start: 18 outliers final: 8 residues processed: 432 average time/residue: 2.1190 time to fit residues: 995.7969 Evaluate side-chains 428 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 416 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 8.9990 chunk 145 optimal weight: 20.0000 chunk 3 optimal weight: 0.7980 chunk 191 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 219 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 230 optimal weight: 10.0000 chunk 64 optimal weight: 0.4980 overall best weight: 4.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 ASN ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** I 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 GLN ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 22551 Z= 0.322 Angle : 0.676 5.205 31033 Z= 0.373 Chirality : 0.049 0.174 3595 Planarity : 0.005 0.038 3826 Dihedral : 12.543 176.997 3948 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.89 % Allowed : 8.77 % Favored : 90.34 % 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: 1.23 (0.16), residues: 2691 helix: 0.95 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.88 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 135 HIS 0.003 0.001 HIS K 86 PHE 0.033 0.004 PHE M 164 TYR 0.017 0.003 TYR F 130 ARG 0.006 0.001 ARG M 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 422 time to evaluate : 2.440 Fit side-chains REVERT: A 58 ASP cc_start: 0.7484 (m-30) cc_final: 0.7196 (m-30) REVERT: A 89 ASP cc_start: 0.8415 (m-30) cc_final: 0.8063 (m-30) REVERT: A 128 MET cc_start: 0.9271 (mmm) cc_final: 0.8916 (mmm) REVERT: A 177 LYS cc_start: 0.8057 (tttm) cc_final: 0.7613 (mppt) REVERT: B 199 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8525 (mtpp) REVERT: D 199 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8389 (mttm) REVERT: E 35 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8110 (mp) REVERT: H 76 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7564 (ttm) REVERT: I 128 MET cc_start: 0.9307 (mmm) cc_final: 0.8990 (mmm) REVERT: J 142 ASN cc_start: 0.8499 (t0) cc_final: 0.8244 (t0) REVERT: J 175 MET cc_start: 0.8369 (tpp) cc_final: 0.8066 (tpp) REVERT: L 65 ILE cc_start: 0.8886 (mt) cc_final: 0.8631 (mt) outliers start: 19 outliers final: 11 residues processed: 434 average time/residue: 2.1205 time to fit residues: 1001.8420 Evaluate side-chains 429 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 414 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain J residue 225 THR Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 100 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 9.9990 chunk 231 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 150 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 257 optimal weight: 8.9990 chunk 213 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 135 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: