Starting phenix.real_space_refine on Sun Sep 29 09:36:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmu_0920/09_2024/6lmu_0920.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmu_0920/09_2024/6lmu_0920.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/6lmu_0920/09_2024/6lmu_0920.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmu_0920/09_2024/6lmu_0920.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmu_0920/09_2024/6lmu_0920.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmu_0920/09_2024/6lmu_0920.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= 0.009 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: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 14553 2.51 5 N 4026 2.21 5 O 3762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 22429 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2039 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 14, 'TRANS': 248} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 54 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J Time building chain proxies: 6.08, per 1000 atoms: 0.27 Number of scatterers: 22429 At special positions: 0 Unit cell: (152.513, 153.874, 100.767, 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 88 16.00 O 3762 8.00 N 4026 7.00 C 14553 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 130 " distance=2.04 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 162 " distance=2.03 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: 4.69 Conformation dependent library (CDL) restraints added in 3.0 seconds 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5522 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 11 sheets defined 69.2% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY A 57 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU A 58 " --> pdb=" O TYR A 54 " (cutoff:3.500A) Proline residue: A 64 - end of helix Processing helix chain 'A' and resid 79 through 88 removed outlier: 4.094A pdb=" N HIS A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 92 removed outlier: 3.640A pdb=" N LYS A 92 " --> pdb=" O ARG A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 92' Processing helix chain 'A' and resid 99 through 113 removed outlier: 3.907A pdb=" N ALA A 113 " --> pdb=" O ARG A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 124 removed outlier: 3.579A pdb=" N ARG A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 135 Processing helix chain 'A' and resid 152 through 158 removed outlier: 4.057A pdb=" N ILE A 156 " --> pdb=" O HIS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 169 through 207 Processing helix chain 'A' and resid 214 through 251 removed outlier: 3.542A pdb=" N ALA A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN A 232 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 274 through 280 Processing helix chain 'A' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP A 302 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY B 57 " --> pdb=" O ASN B 53 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU B 58 " --> pdb=" O TYR B 54 " (cutoff:3.500A) Proline residue: B 64 - end of helix Processing helix chain 'B' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 92 removed outlier: 3.640A pdb=" N LYS B 92 " --> pdb=" O ARG B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 89 through 92' Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.907A pdb=" N ALA B 113 " --> pdb=" O ARG B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 124 removed outlier: 3.580A pdb=" N ARG B 124 " --> pdb=" O ILE B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 135 Processing helix chain 'B' and resid 152 through 158 removed outlier: 4.057A pdb=" N ILE B 156 " --> pdb=" O HIS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 169 through 207 removed outlier: 3.500A pdb=" N ARG B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 251 removed outlier: 3.541A pdb=" N ALA B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 232 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 267 Processing helix chain 'B' and resid 274 through 280 Processing helix chain 'B' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP B 302 " --> pdb=" O ARG B 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU C 58 " --> pdb=" O TYR C 54 " (cutoff:3.500A) Proline residue: C 64 - end of helix Processing helix chain 'C' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 92 removed outlier: 3.640A pdb=" N LYS C 92 " --> pdb=" O ARG C 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 89 through 92' Processing helix chain 'C' and resid 99 through 113 removed outlier: 3.907A pdb=" N ALA C 113 " --> pdb=" O ARG C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 124 removed outlier: 3.579A pdb=" N ARG C 124 " --> pdb=" O ILE C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 135 Processing helix chain 'C' and resid 152 through 158 removed outlier: 4.057A pdb=" N ILE C 156 " --> pdb=" O HIS C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 169 through 207 Processing helix chain 'C' and resid 214 through 251 removed outlier: 3.541A pdb=" N ALA C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN C 232 " --> pdb=" O ASP C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 267 Processing helix chain 'C' and resid 274 through 280 Processing helix chain 'C' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP C 302 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR D 56 " --> pdb=" O ARG D 52 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU D 58 " --> pdb=" O TYR D 54 " (cutoff:3.500A) Proline residue: D 64 - end of helix Processing helix chain 'D' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 92 removed outlier: 3.639A pdb=" N LYS D 92 " --> pdb=" O ARG D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 89 through 92' Processing helix chain 'D' and resid 99 through 113 removed outlier: 3.908A pdb=" N ALA D 113 " --> pdb=" O ARG D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 124 removed outlier: 3.580A pdb=" N ARG D 124 " --> pdb=" O ILE D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 135 Processing helix chain 'D' and resid 152 through 158 removed outlier: 4.057A pdb=" N ILE D 156 " --> pdb=" O HIS D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 168 No H-bonds generated for 'chain 'D' and resid 166 through 168' Processing helix chain 'D' and resid 169 through 207 removed outlier: 3.500A pdb=" N ARG D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 251 removed outlier: 3.541A pdb=" N ALA D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN D 232 " --> pdb=" O ASP D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 274 through 280 Processing helix chain 'D' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP D 302 " --> pdb=" O ARG D 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY E 57 " --> pdb=" O ASN E 53 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU E 58 " --> pdb=" O TYR E 54 " (cutoff:3.500A) Proline residue: E 64 - end of helix Processing helix chain 'E' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS E 88 " --> pdb=" O ALA E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 92 removed outlier: 3.640A pdb=" N LYS E 92 " --> pdb=" O ARG E 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 89 through 92' Processing helix chain 'E' and resid 99 through 113 removed outlier: 3.906A pdb=" N ALA E 113 " --> pdb=" O ARG E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 124 removed outlier: 3.579A pdb=" N ARG E 124 " --> pdb=" O ILE E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 135 Processing helix chain 'E' and resid 152 through 158 removed outlier: 4.058A pdb=" N ILE E 156 " --> pdb=" O HIS E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 168 No H-bonds generated for 'chain 'E' and resid 166 through 168' Processing helix chain 'E' and resid 169 through 207 Processing helix chain 'E' and resid 214 through 251 removed outlier: 3.542A pdb=" N ALA E 225 " --> pdb=" O ALA E 221 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN E 232 " --> pdb=" O ASP E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 267 Processing helix chain 'E' and resid 274 through 280 Processing helix chain 'E' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP E 302 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR F 56 " --> pdb=" O ARG F 52 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY F 57 " --> pdb=" O ASN F 53 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU F 58 " --> pdb=" O TYR F 54 " (cutoff:3.500A) Proline residue: F 64 - end of helix Processing helix chain 'F' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS F 88 " --> pdb=" O ALA F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 92 removed outlier: 3.640A pdb=" N LYS F 92 " --> pdb=" O ARG F 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 89 through 92' Processing helix chain 'F' and resid 99 through 113 removed outlier: 3.907A pdb=" N ALA F 113 " --> pdb=" O ARG F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 124 removed outlier: 3.579A pdb=" N ARG F 124 " --> pdb=" O ILE F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 135 Processing helix chain 'F' and resid 152 through 158 removed outlier: 4.057A pdb=" N ILE F 156 " --> pdb=" O HIS F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 169 through 207 Processing helix chain 'F' and resid 214 through 251 removed outlier: 3.542A pdb=" N ALA F 225 " --> pdb=" O ALA F 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN F 232 " --> pdb=" O ASP F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 267 Processing helix chain 'F' and resid 274 through 280 Processing helix chain 'F' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP F 302 " --> pdb=" O ARG F 298 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR G 56 " --> pdb=" O ARG G 52 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY G 57 " --> pdb=" O ASN G 53 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU G 58 " --> pdb=" O TYR G 54 " (cutoff:3.500A) Proline residue: G 64 - end of helix Processing helix chain 'G' and resid 79 through 88 removed outlier: 4.094A pdb=" N HIS G 88 " --> pdb=" O ALA G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 92 removed outlier: 3.640A pdb=" N LYS G 92 " --> pdb=" O ARG G 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 89 through 92' Processing helix chain 'G' and resid 99 through 113 removed outlier: 3.907A pdb=" N ALA G 113 " --> pdb=" O ARG G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 124 removed outlier: 3.579A pdb=" N ARG G 124 " --> pdb=" O ILE G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 135 Processing helix chain 'G' and resid 152 through 158 removed outlier: 4.057A pdb=" N ILE G 156 " --> pdb=" O HIS G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 168 No H-bonds generated for 'chain 'G' and resid 166 through 168' Processing helix chain 'G' and resid 169 through 207 Processing helix chain 'G' and resid 214 through 251 removed outlier: 3.541A pdb=" N ALA G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN G 232 " --> pdb=" O ASP G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 267 Processing helix chain 'G' and resid 274 through 280 Processing helix chain 'G' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP G 302 " --> pdb=" O ARG G 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR H 56 " --> pdb=" O ARG H 52 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY H 57 " --> pdb=" O ASN H 53 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU H 58 " --> pdb=" O TYR H 54 " (cutoff:3.500A) Proline residue: H 64 - end of helix Processing helix chain 'H' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS H 88 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 92 removed outlier: 3.639A pdb=" N LYS H 92 " --> pdb=" O ARG H 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 89 through 92' Processing helix chain 'H' and resid 99 through 113 removed outlier: 3.907A pdb=" N ALA H 113 " --> pdb=" O ARG H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 124 removed outlier: 3.579A pdb=" N ARG H 124 " --> pdb=" O ILE H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 135 Processing helix chain 'H' and resid 152 through 158 removed outlier: 4.058A pdb=" N ILE H 156 " --> pdb=" O HIS H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 169 through 207 Processing helix chain 'H' and resid 214 through 251 removed outlier: 3.542A pdb=" N ALA H 225 " --> pdb=" O ALA H 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN H 232 " --> pdb=" O ASP H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 267 Processing helix chain 'H' and resid 274 through 280 Processing helix chain 'H' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP H 302 " --> pdb=" O ARG H 298 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR I 56 " --> pdb=" O ARG I 52 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY I 57 " --> pdb=" O ASN I 53 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU I 58 " --> pdb=" O TYR I 54 " (cutoff:3.500A) Proline residue: I 64 - end of helix Processing helix chain 'I' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS I 88 " --> pdb=" O ALA I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 92 removed outlier: 3.639A pdb=" N LYS I 92 " --> pdb=" O ARG I 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 89 through 92' Processing helix chain 'I' and resid 99 through 113 removed outlier: 3.908A pdb=" N ALA I 113 " --> pdb=" O ARG I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 124 removed outlier: 3.580A pdb=" N ARG I 124 " --> pdb=" O ILE I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 135 Processing helix chain 'I' and resid 152 through 158 removed outlier: 4.057A pdb=" N ILE I 156 " --> pdb=" O HIS I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 168 No H-bonds generated for 'chain 'I' and resid 166 through 168' Processing helix chain 'I' and resid 169 through 207 Processing helix chain 'I' and resid 214 through 251 removed outlier: 3.541A pdb=" N ALA I 225 " --> pdb=" O ALA I 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN I 232 " --> pdb=" O ASP I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 257 through 267 Processing helix chain 'I' and resid 274 through 280 Processing helix chain 'I' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP I 302 " --> pdb=" O ARG I 298 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR J 56 " --> pdb=" O ARG J 52 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY J 57 " --> pdb=" O ASN J 53 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU J 58 " --> pdb=" O TYR J 54 " (cutoff:3.500A) Proline residue: J 64 - end of helix Processing helix chain 'J' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS J 88 " --> pdb=" O ALA J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 92 removed outlier: 3.640A pdb=" N LYS J 92 " --> pdb=" O ARG J 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 89 through 92' Processing helix chain 'J' and resid 99 through 113 removed outlier: 3.907A pdb=" N ALA J 113 " --> pdb=" O ARG J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 124 removed outlier: 3.579A pdb=" N ARG J 124 " --> pdb=" O ILE J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 135 Processing helix chain 'J' and resid 152 through 158 removed outlier: 4.057A pdb=" N ILE J 156 " --> pdb=" O HIS J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 168 No H-bonds generated for 'chain 'J' and resid 166 through 168' Processing helix chain 'J' and resid 169 through 207 Processing helix chain 'J' and resid 214 through 251 removed outlier: 3.542A pdb=" N ALA J 225 " --> pdb=" O ALA J 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN J 232 " --> pdb=" O ASP J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 257 through 267 Processing helix chain 'J' and resid 274 through 280 Processing helix chain 'J' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP J 302 " --> pdb=" O ARG J 298 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY K 57 " --> pdb=" O ASN K 53 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU K 58 " --> pdb=" O TYR K 54 " (cutoff:3.500A) Proline residue: K 64 - end of helix Processing helix chain 'K' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS K 88 " --> pdb=" O ALA K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 92 removed outlier: 3.640A pdb=" N LYS K 92 " --> pdb=" O ARG K 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 89 through 92' Processing helix chain 'K' and resid 99 through 113 removed outlier: 3.907A pdb=" N ALA K 113 " --> pdb=" O ARG K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 124 removed outlier: 3.580A pdb=" N ARG K 124 " --> pdb=" O ILE K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 135 Processing helix chain 'K' and resid 152 through 158 removed outlier: 4.058A pdb=" N ILE K 156 " --> pdb=" O HIS K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 168 No H-bonds generated for 'chain 'K' and resid 166 through 168' Processing helix chain 'K' and resid 169 through 207 Processing helix chain 'K' and resid 214 through 251 removed outlier: 3.542A pdb=" N ALA K 225 " --> pdb=" O ALA K 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN K 232 " --> pdb=" O ASP K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 267 Processing helix chain 'K' and resid 274 through 280 Processing helix chain 'K' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP K 302 " --> pdb=" O ARG K 298 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 288 through 289 removed outlier: 3.845A pdb=" N ARG A 288 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 295 " --> pdb=" O ARG A 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 288 through 289 removed outlier: 3.844A pdb=" N ARG B 288 " --> pdb=" O LEU B 295 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 295 " --> pdb=" O ARG B 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 288 through 289 removed outlier: 3.844A pdb=" N ARG C 288 " --> pdb=" O LEU C 295 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 295 " --> pdb=" O ARG C 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 288 through 289 removed outlier: 3.844A pdb=" N ARG D 288 " --> pdb=" O LEU D 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU D 295 " --> pdb=" O ARG D 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 288 through 289 removed outlier: 3.845A pdb=" N ARG E 288 " --> pdb=" O LEU E 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU E 295 " --> pdb=" O ARG E 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 288 through 289 removed outlier: 3.844A pdb=" N ARG F 288 " --> pdb=" O LEU F 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU F 295 " --> pdb=" O ARG F 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 288 through 289 removed outlier: 3.845A pdb=" N ARG G 288 " --> pdb=" O LEU G 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU G 295 " --> pdb=" O ARG G 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'H' and resid 288 through 289 removed outlier: 3.845A pdb=" N ARG H 288 " --> pdb=" O LEU H 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU H 295 " --> pdb=" O ARG H 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'I' and resid 288 through 289 removed outlier: 3.844A pdb=" N ARG I 288 " --> pdb=" O LEU I 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU I 295 " --> pdb=" O ARG I 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'J' and resid 288 through 289 removed outlier: 3.844A pdb=" N ARG J 288 " --> pdb=" O LEU J 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU J 295 " --> pdb=" O ARG J 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 288 through 289 removed outlier: 3.844A pdb=" N ARG K 288 " --> pdb=" O LEU K 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU K 295 " --> pdb=" O ARG K 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 1307 hydrogen bonds defined for protein. 3855 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: 5.91 Time building geometry restraints manager: 5.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7205 1.34 - 1.46: 5886 1.46 - 1.58: 9888 1.58 - 1.71: 0 1.71 - 1.83: 88 Bond restraints: 23067 Sorted by residual: bond pdb=" CB THR C 234 " pdb=" CG2 THR C 234 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.07e+00 bond pdb=" CB THR F 234 " pdb=" CG2 THR F 234 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.07e+00 bond pdb=" CB THR G 234 " pdb=" CG2 THR G 234 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.07e+00 bond pdb=" CB THR H 234 " pdb=" CG2 THR H 234 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.06e+00 bond pdb=" CB THR E 234 " pdb=" CG2 THR E 234 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.06e+00 ... (remaining 23062 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 28716 1.74 - 3.47: 2077 3.47 - 5.21: 514 5.21 - 6.95: 164 6.95 - 8.68: 55 Bond angle restraints: 31526 Sorted by residual: angle pdb=" C ASN H 290 " pdb=" N GLN H 291 " pdb=" CA GLN H 291 " ideal model delta sigma weight residual 121.54 130.22 -8.68 1.91e+00 2.74e-01 2.07e+01 angle pdb=" C ASN I 290 " pdb=" N GLN I 291 " pdb=" CA GLN I 291 " ideal model delta sigma weight residual 121.54 130.22 -8.68 1.91e+00 2.74e-01 2.07e+01 angle pdb=" C ASN B 290 " pdb=" N GLN B 291 " pdb=" CA GLN B 291 " ideal model delta sigma weight residual 121.54 130.22 -8.68 1.91e+00 2.74e-01 2.06e+01 angle pdb=" C ASN C 290 " pdb=" N GLN C 291 " pdb=" CA GLN C 291 " ideal model delta sigma weight residual 121.54 130.22 -8.68 1.91e+00 2.74e-01 2.06e+01 angle pdb=" C ASN J 290 " pdb=" N GLN J 291 " pdb=" CA GLN J 291 " ideal model delta sigma weight residual 121.54 130.21 -8.67 1.91e+00 2.74e-01 2.06e+01 ... (remaining 31521 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 11398 15.12 - 30.24: 1429 30.24 - 45.36: 509 45.36 - 60.48: 119 60.48 - 75.61: 37 Dihedral angle restraints: 13492 sinusoidal: 4967 harmonic: 8525 Sorted by residual: dihedral pdb=" CB CYS A 46 " pdb=" SG CYS A 46 " pdb=" SG CYS A 130 " pdb=" CB CYS A 130 " ideal model delta sinusoidal sigma weight residual 93.00 168.61 -75.61 1 1.00e+01 1.00e-02 7.21e+01 dihedral pdb=" CB CYS A 48 " pdb=" SG CYS A 48 " pdb=" SG CYS A 162 " pdb=" CB CYS A 162 " ideal model delta sinusoidal sigma weight residual -86.00 -34.34 -51.66 1 1.00e+01 1.00e-02 3.65e+01 dihedral pdb=" CA ASN A 77 " pdb=" C ASN A 77 " pdb=" N HIS A 78 " pdb=" CA HIS A 78 " ideal model delta harmonic sigma weight residual -180.00 -152.37 -27.63 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 13489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1661 0.036 - 0.071: 1265 0.071 - 0.107: 325 0.107 - 0.143: 203 0.143 - 0.178: 66 Chirality restraints: 3520 Sorted by residual: chirality pdb=" CB VAL B 284 " pdb=" CA VAL B 284 " pdb=" CG1 VAL B 284 " pdb=" CG2 VAL B 284 " both_signs ideal model delta sigma weight residual False -2.63 -2.81 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CB VAL C 284 " pdb=" CA VAL C 284 " pdb=" CG1 VAL C 284 " pdb=" CG2 VAL C 284 " both_signs ideal model delta sigma weight residual False -2.63 -2.81 0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CB VAL I 284 " pdb=" CA VAL I 284 " pdb=" CG1 VAL I 284 " pdb=" CG2 VAL I 284 " both_signs ideal model delta sigma weight residual False -2.63 -2.81 0.18 2.00e-01 2.50e+01 7.86e-01 ... (remaining 3517 not shown) Planarity restraints: 4048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG I 275 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO I 276 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO I 276 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO I 276 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 275 " 0.045 5.00e-02 4.00e+02 6.79e-02 7.38e+00 pdb=" N PRO B 276 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 276 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 276 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 275 " 0.045 5.00e-02 4.00e+02 6.79e-02 7.38e+00 pdb=" N PRO E 276 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO E 276 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 276 " 0.038 5.00e-02 4.00e+02 ... (remaining 4045 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 218 2.61 - 3.18: 18698 3.18 - 3.75: 34284 3.75 - 4.33: 44895 4.33 - 4.90: 73227 Nonbonded interactions: 171322 Sorted by model distance: nonbonded pdb=" SG CYS K 48 " pdb=" SG CYS K 162 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS D 48 " pdb=" SG CYS D 162 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS F 48 " pdb=" SG CYS F 162 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS J 48 " pdb=" SG CYS J 162 " model vdw 2.034 3.760 nonbonded pdb=" SG CYS B 48 " pdb=" SG CYS B 162 " model vdw 2.034 3.760 ... (remaining 171317 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: 3.140 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.370 Process input model: 37.440 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.050 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 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 : 0.010 0.067 23067 Z= 0.660 Angle : 1.157 8.683 31526 Z= 0.647 Chirality : 0.057 0.178 3520 Planarity : 0.007 0.068 4048 Dihedral : 16.070 69.241 7964 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 1.50 % Allowed : 14.50 % Favored : 84.00 % 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: -5.98 (0.11), residues: 2871 helix: -4.07 (0.06), residues: 1749 sheet: None (None), residues: 0 loop : -3.54 (0.16), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 220 HIS 0.008 0.002 HIS D 88 PHE 0.016 0.003 PHE F 253 TYR 0.033 0.004 TYR E 182 ARG 0.006 0.001 ARG K 178 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 320 time to evaluate : 2.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.7632 (pp20) cc_final: 0.6947 (pp20) REVERT: A 277 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7522 (mm110) REVERT: B 262 GLU cc_start: 0.7462 (pp20) cc_final: 0.6827 (pp20) REVERT: D 293 LEU cc_start: 0.7867 (mt) cc_final: 0.7644 (mt) REVERT: E 76 ASN cc_start: 0.6340 (p0) cc_final: 0.6001 (p0) REVERT: E 212 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8372 (pp) REVERT: E 301 LYS cc_start: 0.8710 (ttpp) cc_final: 0.8468 (ttpp) REVERT: F 76 ASN cc_start: 0.6366 (p0) cc_final: 0.6111 (p0) REVERT: F 277 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7565 (mm110) REVERT: G 76 ASN cc_start: 0.6387 (p0) cc_final: 0.6157 (p0) REVERT: H 76 ASN cc_start: 0.6463 (p0) cc_final: 0.6165 (p0) REVERT: H 277 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7272 (mm110) REVERT: I 71 ILE cc_start: 0.8816 (mt) cc_final: 0.8614 (mt) REVERT: I 76 ASN cc_start: 0.6460 (p0) cc_final: 0.5968 (p0) REVERT: I 301 LYS cc_start: 0.8953 (ttpp) cc_final: 0.8709 (ttpt) REVERT: J 76 ASN cc_start: 0.6577 (p0) cc_final: 0.6260 (p0) outliers start: 33 outliers final: 25 residues processed: 349 average time/residue: 0.3070 time to fit residues: 173.4617 Evaluate side-chains 280 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 254 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 46 CYS Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain G residue 46 CYS Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 195 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 241 optimal weight: 5.9990 chunk 216 optimal weight: 0.2980 chunk 120 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 146 optimal weight: 20.0000 chunk 115 optimal weight: 5.9990 chunk 224 optimal weight: 7.9990 chunk 86 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 259 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN A 300 HIS B 246 ASN B 300 HIS C 246 ASN C 277 GLN C 300 HIS D 45 HIS D 246 ASN D 300 HIS E 246 ASN E 300 HIS F 246 ASN F 300 HIS G 246 ASN G 300 HIS H 246 ASN H 300 HIS I 246 ASN I 300 HIS J 246 ASN J 277 GLN J 300 HIS K 246 ASN K 300 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23067 Z= 0.215 Angle : 0.722 8.625 31526 Z= 0.383 Chirality : 0.040 0.118 3520 Planarity : 0.006 0.045 4048 Dihedral : 6.064 51.654 3231 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.64 % Allowed : 14.77 % Favored : 82.59 % 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: -2.79 (0.14), residues: 2871 helix: -1.17 (0.11), residues: 1815 sheet: None (None), residues: 0 loop : -2.99 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 220 HIS 0.005 0.001 HIS G 238 PHE 0.017 0.002 PHE B 200 TYR 0.017 0.002 TYR I 285 ARG 0.003 0.000 ARG C 181 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 304 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 HIS cc_start: 0.7603 (t-90) cc_final: 0.6826 (t-90) REVERT: A 81 ASN cc_start: 0.7795 (m-40) cc_final: 0.7361 (t0) REVERT: A 181 ARG cc_start: 0.7119 (mmm160) cc_final: 0.6446 (mmt180) REVERT: A 262 GLU cc_start: 0.7560 (pp20) cc_final: 0.6658 (pp20) REVERT: A 266 ASN cc_start: 0.7668 (m-40) cc_final: 0.7078 (m110) REVERT: A 277 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7293 (tt0) REVERT: A 288 ARG cc_start: 0.7786 (mtp-110) cc_final: 0.7582 (mtp85) REVERT: B 81 ASN cc_start: 0.7767 (m-40) cc_final: 0.7358 (t0) REVERT: B 200 PHE cc_start: 0.7833 (t80) cc_final: 0.7573 (t80) REVERT: B 262 GLU cc_start: 0.7173 (pp20) cc_final: 0.6656 (pp20) REVERT: B 266 ASN cc_start: 0.7901 (m-40) cc_final: 0.7619 (m-40) REVERT: B 277 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7235 (tt0) REVERT: C 81 ASN cc_start: 0.7945 (m-40) cc_final: 0.7565 (t0) REVERT: C 262 GLU cc_start: 0.7470 (pp20) cc_final: 0.7087 (pp20) REVERT: D 81 ASN cc_start: 0.7778 (m-40) cc_final: 0.7551 (t0) REVERT: D 198 LEU cc_start: 0.7884 (tp) cc_final: 0.7556 (tp) REVERT: D 277 GLN cc_start: 0.7393 (mm110) cc_final: 0.7184 (tt0) REVERT: D 284 VAL cc_start: 0.6950 (OUTLIER) cc_final: 0.6706 (m) REVERT: E 81 ASN cc_start: 0.7941 (m-40) cc_final: 0.7656 (t0) REVERT: E 212 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8089 (pp) REVERT: E 262 GLU cc_start: 0.7420 (pp20) cc_final: 0.7220 (pp20) REVERT: E 277 GLN cc_start: 0.7504 (mm110) cc_final: 0.7171 (tt0) REVERT: E 301 LYS cc_start: 0.8670 (ttpp) cc_final: 0.8415 (ttpt) REVERT: F 78 HIS cc_start: 0.7480 (t-90) cc_final: 0.6851 (t-90) REVERT: F 81 ASN cc_start: 0.7782 (m-40) cc_final: 0.7384 (t0) REVERT: F 128 TYR cc_start: 0.4757 (p90) cc_final: 0.4405 (p90) REVERT: F 200 PHE cc_start: 0.7856 (t80) cc_final: 0.7439 (t80) REVERT: F 277 GLN cc_start: 0.7693 (mm-40) cc_final: 0.7188 (tt0) REVERT: G 78 HIS cc_start: 0.7357 (t-90) cc_final: 0.6846 (t-90) REVERT: G 81 ASN cc_start: 0.7930 (m-40) cc_final: 0.7423 (t0) REVERT: G 277 GLN cc_start: 0.7663 (mm110) cc_final: 0.7163 (tt0) REVERT: H 78 HIS cc_start: 0.7826 (t-90) cc_final: 0.7284 (t-90) REVERT: H 81 ASN cc_start: 0.7806 (m-40) cc_final: 0.7401 (t0) REVERT: H 262 GLU cc_start: 0.7441 (pp20) cc_final: 0.7232 (pp20) REVERT: I 71 ILE cc_start: 0.8431 (mt) cc_final: 0.8217 (mt) REVERT: I 81 ASN cc_start: 0.7802 (m-40) cc_final: 0.7498 (t0) REVERT: I 277 GLN cc_start: 0.7724 (mm110) cc_final: 0.7320 (tt0) REVERT: I 301 LYS cc_start: 0.9029 (ttpp) cc_final: 0.8668 (ttpp) REVERT: J 200 PHE cc_start: 0.7544 (t80) cc_final: 0.7318 (t80) REVERT: J 266 ASN cc_start: 0.7690 (m-40) cc_final: 0.7488 (m-40) REVERT: J 284 VAL cc_start: 0.6449 (OUTLIER) cc_final: 0.6072 (m) outliers start: 58 outliers final: 26 residues processed: 360 average time/residue: 0.2826 time to fit residues: 166.3144 Evaluate side-chains 285 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 256 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 212 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.52 > 50: distance: 68 - 73: 24.090 distance: 73 - 74: 35.759 distance: 74 - 75: 18.170 distance: 74 - 77: 20.138 distance: 75 - 76: 37.325 distance: 75 - 82: 25.927 distance: 77 - 78: 29.725 distance: 78 - 79: 26.197 distance: 79 - 80: 13.627 distance: 79 - 81: 8.816 distance: 82 - 83: 11.146 distance: 82 - 88: 53.050 distance: 83 - 84: 37.662 distance: 83 - 86: 40.510 distance: 84 - 85: 20.870 distance: 84 - 89: 34.659 distance: 85 - 116: 31.945 distance: 86 - 87: 33.332 distance: 87 - 88: 34.819 distance: 89 - 90: 9.231 distance: 90 - 91: 17.922 distance: 90 - 93: 25.972 distance: 91 - 92: 15.159 distance: 91 - 100: 10.098 distance: 92 - 130: 39.714 distance: 93 - 94: 49.106 distance: 94 - 95: 33.542 distance: 95 - 96: 4.530 distance: 96 - 97: 16.653 distance: 97 - 98: 8.501 distance: 97 - 99: 16.540 distance: 100 - 101: 11.338 distance: 100 - 106: 29.018 distance: 101 - 102: 9.736 distance: 101 - 104: 10.156 distance: 102 - 103: 21.199 distance: 102 - 107: 26.340 distance: 103 - 138: 39.424 distance: 104 - 105: 25.478 distance: 105 - 106: 24.470 distance: 107 - 108: 32.600 distance: 108 - 109: 16.126 distance: 108 - 111: 34.664 distance: 109 - 110: 11.082 distance: 109 - 116: 7.320 distance: 111 - 112: 12.462 distance: 112 - 113: 24.333 distance: 113 - 114: 18.064 distance: 113 - 115: 21.471 distance: 116 - 117: 15.039 distance: 117 - 118: 35.606 distance: 117 - 120: 9.966 distance: 118 - 119: 22.514 distance: 118 - 130: 14.793 distance: 120 - 121: 20.866 distance: 121 - 122: 15.254 distance: 121 - 123: 9.478 distance: 122 - 124: 24.403 distance: 123 - 125: 19.157 distance: 123 - 126: 4.032 distance: 124 - 125: 11.170 distance: 125 - 127: 11.205 distance: 126 - 128: 19.023 distance: 127 - 129: 13.157 distance: 128 - 129: 17.539 distance: 130 - 131: 19.388 distance: 131 - 132: 29.897 distance: 131 - 134: 25.081 distance: 132 - 133: 3.367 distance: 132 - 138: 7.190 distance: 134 - 135: 27.719 distance: 135 - 136: 27.300 distance: 135 - 137: 12.951 distance: 138 - 139: 35.524 distance: 139 - 140: 3.613 distance: 139 - 142: 37.423 distance: 140 - 141: 12.238 distance: 140 - 143: 9.869 distance: 143 - 144: 33.844 distance: 144 - 145: 3.234 distance: 144 - 147: 18.787 distance: 145 - 146: 5.548 distance: 145 - 151: 23.835 distance: 147 - 148: 20.428 distance: 147 - 149: 45.383 distance: 148 - 150: 24.907 distance: 151 - 152: 5.823 distance: 152 - 153: 34.501 distance: 152 - 155: 29.341 distance: 153 - 154: 8.125 distance: 153 - 158: 28.451 distance: 155 - 156: 3.479 distance: 155 - 157: 13.351