Starting phenix.real_space_refine on Tue Jun 25 05:51:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adw_15372/06_2024/8adw_15372.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adw_15372/06_2024/8adw_15372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adw_15372/06_2024/8adw_15372.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adw_15372/06_2024/8adw_15372.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adw_15372/06_2024/8adw_15372.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adw_15372/06_2024/8adw_15372.pdb" } resolution = 2.95 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= 0.002 sd= 0.011 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 20 5.16 5 C 4320 2.51 5 N 1200 2.21 5 O 1380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 6920 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "B" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "C" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "D" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "E" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "F" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "G" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "H" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "I" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "J" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Time building chain proxies: 4.30, per 1000 atoms: 0.62 Number of scatterers: 6920 At special positions: 0 Unit cell: (143.85, 139.65, 45.15, 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 20 16.00 O 1380 8.00 N 1200 7.00 C 4320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.5 seconds 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1700 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 21 sheets defined 0.0% alpha, 42.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.745A pdb=" N PHE A 4 " --> pdb=" O MET B 5 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N PHE B 4 " --> pdb=" O MET C 5 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N PHE C 4 " --> pdb=" O MET D 5 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE D 4 " --> pdb=" O MET E 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 20 removed outlier: 6.246A pdb=" N VAL A 15 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ALA B 18 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA A 17 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N GLU B 20 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA A 19 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL B 15 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ALA C 18 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA B 17 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N GLU C 20 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA B 19 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL C 15 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ALA D 18 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA C 17 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N GLU D 20 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA C 19 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL D 15 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ALA E 18 " --> pdb=" O VAL D 15 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA D 17 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N GLU E 20 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA D 19 " --> pdb=" O GLU E 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AA4, first strand: chain 'A' and resid 27 through 32 removed outlier: 6.361A pdb=" N ALA A 27 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ALA B 30 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA A 29 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LYS B 32 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY A 31 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA B 27 " --> pdb=" O GLU C 28 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ALA C 30 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA B 29 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LYS C 32 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 31 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA C 27 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ALA D 30 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA C 29 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LYS D 32 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLY C 31 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA D 27 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ALA E 30 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA D 29 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LYS E 32 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLY D 31 " --> pdb=" O LYS E 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 35 through 40 removed outlier: 6.740A pdb=" N GLY B 36 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY C 36 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLY D 36 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY E 36 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 48 through 55 Processing sheet with id=AA7, first strand: chain 'A' and resid 61 through 66 Processing sheet with id=AA8, first strand: chain 'A' and resid 70 through 71 removed outlier: 6.280A pdb=" N VAL A 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL B 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL C 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL D 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 74 through 78 Processing sheet with id=AB1, first strand: chain 'A' and resid 87 through 95 removed outlier: 6.098A pdb=" N ILE A 88 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA B 91 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ALA A 90 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLY B 93 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N THR A 92 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N VAL B 95 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N PHE A 94 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE B 88 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA C 91 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ALA B 90 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLY C 93 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N THR B 92 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N VAL C 95 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N PHE B 94 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE C 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA D 91 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ALA C 90 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLY D 93 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N THR C 92 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N VAL D 95 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N PHE C 94 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE D 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA E 91 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ALA D 90 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLY E 93 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N THR D 92 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N VAL E 95 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N PHE D 94 " --> pdb=" O VAL E 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 4 through 5 removed outlier: 6.752A pdb=" N PHE F 4 " --> pdb=" O MET G 5 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE G 4 " --> pdb=" O MET H 5 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE H 4 " --> pdb=" O MET I 5 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE I 4 " --> pdb=" O MET J 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 15 through 20 removed outlier: 6.249A pdb=" N VAL F 15 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ALA G 18 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA F 17 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLU G 20 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA F 19 " --> pdb=" O GLU G 20 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL G 15 " --> pdb=" O VAL H 16 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ALA H 18 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA G 17 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLU H 20 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA G 19 " --> pdb=" O GLU H 20 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL H 15 " --> pdb=" O VAL I 16 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ALA I 18 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA H 17 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLU I 20 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA H 19 " --> pdb=" O GLU I 20 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL I 15 " --> pdb=" O VAL J 16 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ALA J 18 " --> pdb=" O VAL I 15 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA I 17 " --> pdb=" O ALA J 18 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLU J 20 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA I 19 " --> pdb=" O GLU J 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 23 through 24 Processing sheet with id=AB5, first strand: chain 'F' and resid 27 through 32 removed outlier: 6.361A pdb=" N ALA F 27 " --> pdb=" O GLU G 28 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ALA G 30 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA F 29 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LYS G 32 " --> pdb=" O ALA F 29 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY F 31 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA G 27 " --> pdb=" O GLU H 28 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ALA H 30 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA G 29 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N LYS H 32 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY G 31 " --> pdb=" O LYS H 32 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA H 27 " --> pdb=" O GLU I 28 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ALA I 30 " --> pdb=" O ALA H 27 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA H 29 " --> pdb=" O ALA I 30 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LYS I 32 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY H 31 " --> pdb=" O LYS I 32 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA I 27 " --> pdb=" O GLU J 28 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ALA J 30 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA I 29 " --> pdb=" O ALA J 30 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LYS J 32 " --> pdb=" O ALA I 29 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY I 31 " --> pdb=" O LYS J 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 35 through 40 removed outlier: 6.739A pdb=" N GLY G 36 " --> pdb=" O GLU F 35 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY H 36 " --> pdb=" O GLU G 35 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY I 36 " --> pdb=" O GLU H 35 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY J 36 " --> pdb=" O GLU I 35 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 48 through 55 Processing sheet with id=AB8, first strand: chain 'F' and resid 61 through 66 Processing sheet with id=AB9, first strand: chain 'F' and resid 70 through 71 removed outlier: 6.274A pdb=" N VAL F 70 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL G 70 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL H 70 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL I 70 " --> pdb=" O VAL J 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 74 through 77 removed outlier: 6.237A pdb=" N VAL F 74 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL G 77 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA F 76 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL G 74 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL H 77 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA G 76 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL H 74 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL I 77 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA H 76 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL I 74 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL J 77 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA I 76 " --> pdb=" O VAL J 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'F' and resid 82 through 83 removed outlier: 6.609A pdb=" N VAL F 82 " --> pdb=" O GLU G 83 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL G 82 " --> pdb=" O GLU H 83 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL H 82 " --> pdb=" O GLU I 83 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL I 82 " --> pdb=" O GLU J 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 87 through 95 removed outlier: 6.093A pdb=" N ILE F 88 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ALA G 91 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ALA F 90 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLY G 93 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N THR F 92 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 10.741A pdb=" N VAL G 95 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N PHE F 94 " --> pdb=" O VAL G 95 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE G 88 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ALA H 91 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ALA G 90 " --> pdb=" O ALA H 91 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLY H 93 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N THR G 92 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 10.741A pdb=" N VAL H 95 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N PHE G 94 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE H 88 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ALA I 91 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ALA H 90 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLY I 93 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N THR H 92 " --> pdb=" O GLY I 93 " (cutoff:3.500A) removed outlier: 10.741A pdb=" N VAL I 95 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N PHE H 94 " --> pdb=" O VAL I 95 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE I 88 " --> pdb=" O ALA J 89 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ALA J 91 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ALA I 90 " --> pdb=" O ALA J 91 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLY J 93 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N THR I 92 " --> pdb=" O GLY J 93 " (cutoff:3.500A) removed outlier: 10.740A pdb=" N VAL J 95 " --> pdb=" O THR I 92 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N PHE I 94 " --> pdb=" O VAL J 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 152 hydrogen bonds defined for protein. 456 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: 1.78 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1423 1.32 - 1.44: 1262 1.44 - 1.56: 4225 1.56 - 1.68: 0 1.68 - 1.80: 40 Bond restraints: 6950 Sorted by residual: bond pdb=" CA LYS F 80 " pdb=" C LYS F 80 " ideal model delta sigma weight residual 1.521 1.474 0.047 1.24e-02 6.50e+03 1.44e+01 bond pdb=" CA LYS G 80 " pdb=" C LYS G 80 " ideal model delta sigma weight residual 1.521 1.474 0.047 1.24e-02 6.50e+03 1.41e+01 bond pdb=" CA LYS H 80 " pdb=" C LYS H 80 " ideal model delta sigma weight residual 1.521 1.474 0.047 1.24e-02 6.50e+03 1.41e+01 bond pdb=" CA LYS J 80 " pdb=" C LYS J 80 " ideal model delta sigma weight residual 1.521 1.475 0.046 1.24e-02 6.50e+03 1.38e+01 bond pdb=" CA LYS I 80 " pdb=" C LYS I 80 " ideal model delta sigma weight residual 1.521 1.475 0.046 1.24e-02 6.50e+03 1.36e+01 ... (remaining 6945 not shown) Histogram of bond angle deviations from ideal: 100.91 - 106.98: 155 106.98 - 113.04: 3884 113.04 - 119.11: 1888 119.11 - 125.18: 3373 125.18 - 131.24: 20 Bond angle restraints: 9320 Sorted by residual: angle pdb=" N LYS A 60 " pdb=" CA LYS A 60 " pdb=" C LYS A 60 " ideal model delta sigma weight residual 112.12 102.90 9.22 1.34e+00 5.57e-01 4.74e+01 angle pdb=" N LYS B 60 " pdb=" CA LYS B 60 " pdb=" C LYS B 60 " ideal model delta sigma weight residual 112.12 102.91 9.21 1.34e+00 5.57e-01 4.73e+01 angle pdb=" N LYS J 60 " pdb=" CA LYS J 60 " pdb=" C LYS J 60 " ideal model delta sigma weight residual 112.12 102.91 9.21 1.34e+00 5.57e-01 4.73e+01 angle pdb=" N LYS E 60 " pdb=" CA LYS E 60 " pdb=" C LYS E 60 " ideal model delta sigma weight residual 112.12 102.91 9.21 1.34e+00 5.57e-01 4.72e+01 angle pdb=" N LYS H 60 " pdb=" CA LYS H 60 " pdb=" C LYS H 60 " ideal model delta sigma weight residual 112.12 102.92 9.20 1.34e+00 5.57e-01 4.71e+01 ... (remaining 9315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 3495 17.81 - 35.62: 335 35.62 - 53.42: 250 53.42 - 71.23: 85 71.23 - 89.04: 15 Dihedral angle restraints: 4180 sinusoidal: 1490 harmonic: 2690 Sorted by residual: dihedral pdb=" CB GLU A 57 " pdb=" CG GLU A 57 " pdb=" CD GLU A 57 " pdb=" OE1 GLU A 57 " ideal model delta sinusoidal sigma weight residual 0.00 -89.04 89.04 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU E 57 " pdb=" CG GLU E 57 " pdb=" CD GLU E 57 " pdb=" OE1 GLU E 57 " ideal model delta sinusoidal sigma weight residual 0.00 -89.04 89.04 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU B 57 " pdb=" CG GLU B 57 " pdb=" CD GLU B 57 " pdb=" OE1 GLU B 57 " ideal model delta sinusoidal sigma weight residual 0.00 -89.04 89.04 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 4177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 866 0.066 - 0.132: 229 0.132 - 0.198: 40 0.198 - 0.263: 10 0.263 - 0.329: 15 Chirality restraints: 1160 Sorted by residual: chirality pdb=" CA PHE J 94 " pdb=" N PHE J 94 " pdb=" C PHE J 94 " pdb=" CB PHE J 94 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA PHE H 94 " pdb=" N PHE H 94 " pdb=" C PHE H 94 " pdb=" CB PHE H 94 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA PHE D 94 " pdb=" N PHE D 94 " pdb=" C PHE D 94 " pdb=" CB PHE D 94 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 1157 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS F 60 " 0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C LYS F 60 " -0.067 2.00e-02 2.50e+03 pdb=" O LYS F 60 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU F 61 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 60 " -0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C LYS B 60 " 0.066 2.00e-02 2.50e+03 pdb=" O LYS B 60 " -0.025 2.00e-02 2.50e+03 pdb=" N GLU B 61 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS I 60 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C LYS I 60 " -0.066 2.00e-02 2.50e+03 pdb=" O LYS I 60 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU I 61 " 0.022 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 3280 2.96 - 3.44: 6194 3.44 - 3.93: 11912 3.93 - 4.41: 14300 4.41 - 4.90: 25161 Nonbonded interactions: 60847 Sorted by model distance: nonbonded pdb=" O GLY F 84 " pdb=" O ALA G 85 " model vdw 2.469 3.040 nonbonded pdb=" O GLY G 84 " pdb=" O ALA H 85 " model vdw 2.469 3.040 nonbonded pdb=" O GLY I 84 " pdb=" O ALA J 85 " model vdw 2.469 3.040 nonbonded pdb=" O GLY H 84 " pdb=" O ALA I 85 " model vdw 2.469 3.040 nonbonded pdb=" O GLY B 84 " pdb=" O ALA C 85 " model vdw 2.472 3.040 ... (remaining 60842 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.650 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: 3.330 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.080 Find NCS groups from input model: 0.450 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:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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 : 0.009 0.060 6950 Z= 0.644 Angle : 1.463 12.618 9320 Z= 0.911 Chirality : 0.073 0.329 1160 Planarity : 0.006 0.038 1170 Dihedral : 22.424 89.039 2480 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 23.33 % Allowed : 11.45 % Favored : 65.22 % 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: -4.02 (0.21), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.052 0.009 PHE F 94 TYR 0.003 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 149 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.7128 (mt-10) REVERT: A 98 ASP cc_start: 0.7216 (OUTLIER) cc_final: 0.6886 (m-30) REVERT: B 92 THR cc_start: 0.8341 (m) cc_final: 0.7941 (p) REVERT: C 5 MET cc_start: 0.7423 (ttm) cc_final: 0.7190 (ttt) REVERT: D 28 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: D 92 THR cc_start: 0.8456 (m) cc_final: 0.8055 (p) REVERT: D 98 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.6964 (m-30) REVERT: E 5 MET cc_start: 0.7329 (ttm) cc_final: 0.7067 (ttt) REVERT: E 12 LYS cc_start: 0.6706 (OUTLIER) cc_final: 0.5540 (pmtt) REVERT: F 5 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7587 (ttt) REVERT: F 28 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7155 (mt-10) REVERT: F 98 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.7021 (m-30) REVERT: H 5 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.7216 (ttt) REVERT: H 20 GLU cc_start: 0.7452 (mp0) cc_final: 0.7243 (mp0) REVERT: I 28 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: I 98 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.6820 (m-30) REVERT: J 5 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.7070 (ttt) REVERT: J 12 LYS cc_start: 0.6839 (OUTLIER) cc_final: 0.5668 (pmtt) REVERT: J 20 GLU cc_start: 0.7307 (mp0) cc_final: 0.7093 (mp0) outliers start: 161 outliers final: 17 residues processed: 245 average time/residue: 1.1519 time to fit residues: 296.5298 Evaluate side-chains 139 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 109 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 2 ASP Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 5 MET Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain G residue 2 ASP Chi-restraints excluded: chain H residue 2 ASP Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 2 ASP Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain J residue 2 ASP Chi-restraints excluded: chain J residue 5 MET Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.0542 > 50: distance: 49 - 135: 30.527 distance: 52 - 143: 17.372 distance: 64 - 146: 8.104 distance: 86 - 89: 4.494 distance: 89 - 90: 4.063 distance: 90 - 91: 5.674 distance: 90 - 93: 9.756 distance: 91 - 92: 8.059 distance: 91 - 94: 16.740 distance: 94 - 95: 21.585 distance: 95 - 96: 6.759 distance: 96 - 97: 21.480 distance: 96 - 98: 5.858 distance: 98 - 99: 13.775 distance: 99 - 100: 13.007 distance: 99 - 102: 5.809 distance: 100 - 101: 10.049 distance: 100 - 107: 20.225 distance: 102 - 103: 8.012 distance: 103 - 104: 22.296 distance: 104 - 105: 21.714 distance: 105 - 106: 13.783 distance: 107 - 108: 6.625 distance: 108 - 109: 8.385 distance: 108 - 111: 5.396 distance: 109 - 110: 25.653 distance: 109 - 114: 10.639 distance: 111 - 112: 8.106 distance: 111 - 113: 3.813 distance: 114 - 115: 16.695 distance: 115 - 118: 19.315 distance: 116 - 117: 33.255 distance: 116 - 123: 23.053 distance: 118 - 119: 7.066 distance: 119 - 120: 20.123 distance: 120 - 121: 14.693 distance: 121 - 122: 11.575 distance: 123 - 124: 17.260 distance: 124 - 125: 16.392 distance: 124 - 127: 38.917 distance: 125 - 126: 38.158 distance: 125 - 132: 27.604 distance: 127 - 128: 29.027 distance: 128 - 129: 24.674 distance: 129 - 130: 57.044 distance: 129 - 131: 6.724 distance: 132 - 133: 11.635 distance: 133 - 134: 18.172 distance: 134 - 135: 23.960 distance: 134 - 136: 47.713 distance: 136 - 137: 4.298 distance: 136 - 235: 27.454 distance: 137 - 138: 7.770 distance: 137 - 140: 13.259 distance: 138 - 139: 14.348 distance: 138 - 143: 19.549 distance: 139 - 243: 30.224 distance: 140 - 141: 14.119 distance: 140 - 142: 20.850 distance: 143 - 144: 15.188 distance: 144 - 145: 10.474 distance: 144 - 147: 22.192 distance: 145 - 146: 4.595 distance: 145 - 151: 7.995 distance: 147 - 148: 12.160 distance: 148 - 149: 11.815 distance: 148 - 150: 50.406 distance: 151 - 152: 3.602 distance: 151 - 246: 16.883 distance: 152 - 153: 6.987 distance: 152 - 155: 7.448 distance: 153 - 154: 4.660 distance: 153 - 163: 6.538 distance: 154 - 262: 14.658 distance: 155 - 156: 11.195 distance: 156 - 157: 10.011 distance: 156 - 158: 10.879 distance: 157 - 159: 9.352 distance: 158 - 160: 4.470 distance: 159 - 161: 10.494 distance: 160 - 161: 3.016 distance: 161 - 162: 34.331