Starting phenix.real_space_refine on Sun Mar 17 21:45:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fj5_29215/03_2024/8fj5_29215.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fj5_29215/03_2024/8fj5_29215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fj5_29215/03_2024/8fj5_29215.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fj5_29215/03_2024/8fj5_29215.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fj5_29215/03_2024/8fj5_29215.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fj5_29215/03_2024/8fj5_29215.pdb" } resolution = 2.9 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 ------------------------------------------------------------------------------- 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= 0.005 sd= 0.077 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 11740 2.51 5 N 2980 2.21 5 O 4240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 56": "OD1" <-> "OD2" Residue "A ASP 94": "OD1" <-> "OD2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B ASP 94": "OD1" <-> "OD2" Residue "C ASP 56": "OD1" <-> "OD2" Residue "C ASP 94": "OD1" <-> "OD2" Residue "D ASP 56": "OD1" <-> "OD2" Residue "D ASP 94": "OD1" <-> "OD2" Residue "E ASP 56": "OD1" <-> "OD2" Residue "E ASP 94": "OD1" <-> "OD2" Residue "F ASP 56": "OD1" <-> "OD2" Residue "F ASP 94": "OD1" <-> "OD2" Residue "G ASP 56": "OD1" <-> "OD2" Residue "G ASP 94": "OD1" <-> "OD2" Residue "H ASP 56": "OD1" <-> "OD2" Residue "H ASP 94": "OD1" <-> "OD2" Residue "I ASP 56": "OD1" <-> "OD2" Residue "I ASP 94": "OD1" <-> "OD2" Residue "J ASP 56": "OD1" <-> "OD2" Residue "J ASP 94": "OD1" <-> "OD2" Residue "K ASP 56": "OD1" <-> "OD2" Residue "K ASP 94": "OD1" <-> "OD2" Residue "L ASP 56": "OD1" <-> "OD2" Residue "L ASP 94": "OD1" <-> "OD2" Residue "M ASP 56": "OD1" <-> "OD2" Residue "M ASP 94": "OD1" <-> "OD2" Residue "N ASP 56": "OD1" <-> "OD2" Residue "N ASP 94": "OD1" <-> "OD2" Residue "O ASP 56": "OD1" <-> "OD2" Residue "O ASP 94": "OD1" <-> "OD2" Residue "P ASP 56": "OD1" <-> "OD2" Residue "P ASP 94": "OD1" <-> "OD2" Residue "Q ASP 56": "OD1" <-> "OD2" Residue "Q ASP 94": "OD1" <-> "OD2" Residue "R ASP 56": "OD1" <-> "OD2" Residue "R ASP 94": "OD1" <-> "OD2" Residue "S ASP 56": "OD1" <-> "OD2" Residue "S ASP 94": "OD1" <-> "OD2" Residue "T ASP 56": "OD1" <-> "OD2" Residue "T ASP 94": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18980 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 949 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "B" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 949 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "C" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 949 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "D" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 949 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "E" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 949 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "F" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 949 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "G" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 949 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "H" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 949 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "I" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 949 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "J" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 949 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "K" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 949 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "L" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 949 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "M" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 949 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "N" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 949 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "O" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 949 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "P" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 949 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "Q" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 949 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "R" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 949 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "S" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 949 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "T" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 949 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Time building chain proxies: 10.18, per 1000 atoms: 0.54 Number of scatterers: 18980 At special positions: 0 Unit cell: (97.44, 98.56, 202.72, 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 4240 8.00 N 2980 7.00 C 11740 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: 7.17 Conformation dependent library (CDL) restraints added in 3.6 seconds 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4720 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 60 sheets defined 26.4% alpha, 45.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 removed outlier: 3.610A pdb=" N ILE A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP A 96 " --> pdb=" O TRP A 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 96 removed outlier: 3.747A pdb=" N ASP B 96 " --> pdb=" O TRP B 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 96 removed outlier: 3.747A pdb=" N ASP C 96 " --> pdb=" O TRP C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 96 removed outlier: 3.747A pdb=" N ASP D 96 " --> pdb=" O TRP D 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 96 removed outlier: 3.747A pdb=" N ASP E 96 " --> pdb=" O TRP E 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP F 96 " --> pdb=" O TRP F 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP G 96 " --> pdb=" O TRP G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE H 28 " --> pdb=" O ALA H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP H 96 " --> pdb=" O TRP H 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE I 28 " --> pdb=" O ALA I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP I 96 " --> pdb=" O TRP I 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE J 28 " --> pdb=" O ALA J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP J 96 " --> pdb=" O TRP J 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE K 28 " --> pdb=" O ALA K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 96 removed outlier: 3.747A pdb=" N ASP K 96 " --> pdb=" O TRP K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE L 28 " --> pdb=" O ALA L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP L 96 " --> pdb=" O TRP L 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE M 28 " --> pdb=" O ALA M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 96 removed outlier: 3.747A pdb=" N ASP M 96 " --> pdb=" O TRP M 92 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE N 28 " --> pdb=" O ALA N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP N 96 " --> pdb=" O TRP N 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE O 28 " --> pdb=" O ALA O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP O 96 " --> pdb=" O TRP O 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP P 96 " --> pdb=" O TRP P 92 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE Q 28 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP Q 96 " --> pdb=" O TRP Q 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP R 96 " --> pdb=" O TRP R 92 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE S 28 " --> pdb=" O ALA S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP S 96 " --> pdb=" O TRP S 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE T 28 " --> pdb=" O ALA T 24 " (cutoff:3.500A) Processing helix chain 'T' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP T 96 " --> pdb=" O TRP T 92 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 58 removed outlier: 6.759A pdb=" N SER A 52 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN A 63 " --> pdb=" O THR A 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 58 removed outlier: 6.759A pdb=" N SER A 52 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN A 63 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR A 65 " --> pdb=" O TRP I 141 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP I 141 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR A 67 " --> pdb=" O GLN I 139 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN I 139 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU A 69 " --> pdb=" O THR I 137 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR I 137 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL I 125 " --> pdb=" O LEU I 138 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER I 140 " --> pdb=" O VAL I 123 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL I 123 " --> pdb=" O SER I 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 75 Processing sheet with id=AA4, first strand: chain 'A' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL A 123 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER A 140 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 125 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 137 " --> pdb=" O GLU N 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU N 69 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN A 139 " --> pdb=" O THR N 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR N 67 " --> pdb=" O GLN A 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP A 141 " --> pdb=" O THR N 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR N 65 " --> pdb=" O TRP A 141 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN N 63 " --> pdb=" O THR N 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER N 52 " --> pdb=" O GLU N 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL A 123 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER A 140 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 125 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 137 " --> pdb=" O GLU N 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU N 69 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN A 139 " --> pdb=" O THR N 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR N 67 " --> pdb=" O GLN A 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP A 141 " --> pdb=" O THR N 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR N 65 " --> pdb=" O TRP A 141 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 51 through 58 removed outlier: 6.759A pdb=" N SER B 52 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN B 63 " --> pdb=" O THR B 58 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 74 through 75 Processing sheet with id=AA8, first strand: chain 'B' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL B 123 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER B 140 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 125 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 137 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU E 69 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN B 139 " --> pdb=" O THR E 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR E 67 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP B 141 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR E 65 " --> pdb=" O TRP B 141 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN E 63 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER E 52 " --> pdb=" O GLU E 69 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL B 123 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER B 140 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 125 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 137 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU E 69 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN B 139 " --> pdb=" O THR E 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR E 67 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP B 141 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR E 65 " --> pdb=" O TRP B 141 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 51 through 58 removed outlier: 6.758A pdb=" N SER C 52 " --> pdb=" O GLU C 69 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN C 63 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 74 through 75 Processing sheet with id=AB3, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.461A pdb=" N VAL C 123 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER C 140 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 125 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C 137 " --> pdb=" O GLU F 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU F 69 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN C 139 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR F 67 " --> pdb=" O GLN C 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP C 141 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR F 65 " --> pdb=" O TRP C 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN F 63 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER F 52 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.461A pdb=" N VAL C 123 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER C 140 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 125 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C 137 " --> pdb=" O GLU F 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU F 69 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN C 139 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR F 67 " --> pdb=" O GLN C 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP C 141 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR F 65 " --> pdb=" O TRP C 141 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 51 through 58 removed outlier: 6.760A pdb=" N SER D 52 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN D 63 " --> pdb=" O THR D 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 74 through 75 Processing sheet with id=AB7, first strand: chain 'D' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL D 123 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER D 140 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL D 125 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR D 137 " --> pdb=" O GLU G 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU G 69 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN D 139 " --> pdb=" O THR G 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR G 67 " --> pdb=" O GLN D 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP D 141 " --> pdb=" O THR G 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR G 65 " --> pdb=" O TRP D 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN G 63 " --> pdb=" O THR G 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER G 52 " --> pdb=" O GLU G 69 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL D 123 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER D 140 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL D 125 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR D 137 " --> pdb=" O GLU G 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU G 69 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN D 139 " --> pdb=" O THR G 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR G 67 " --> pdb=" O GLN D 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP D 141 " --> pdb=" O THR G 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR G 65 " --> pdb=" O TRP D 141 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 74 through 75 Processing sheet with id=AC1, first strand: chain 'E' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL E 123 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER E 140 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL E 125 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR E 137 " --> pdb=" O GLU H 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU H 69 " --> pdb=" O THR E 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN E 139 " --> pdb=" O THR H 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR H 67 " --> pdb=" O GLN E 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP E 141 " --> pdb=" O THR H 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR H 65 " --> pdb=" O TRP E 141 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN H 63 " --> pdb=" O THR H 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER H 52 " --> pdb=" O GLU H 69 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL E 123 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER E 140 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL E 125 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR E 137 " --> pdb=" O GLU H 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU H 69 " --> pdb=" O THR E 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN E 139 " --> pdb=" O THR H 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR H 67 " --> pdb=" O GLN E 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP E 141 " --> pdb=" O THR H 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR H 65 " --> pdb=" O TRP E 141 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 74 through 75 Processing sheet with id=AC4, first strand: chain 'F' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL F 123 " --> pdb=" O SER F 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER F 140 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL F 125 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR F 137 " --> pdb=" O GLU I 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU I 69 " --> pdb=" O THR F 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN F 139 " --> pdb=" O THR I 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR I 67 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP F 141 " --> pdb=" O THR I 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR I 65 " --> pdb=" O TRP F 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN I 63 " --> pdb=" O THR I 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER I 52 " --> pdb=" O GLU I 69 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL F 123 " --> pdb=" O SER F 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER F 140 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL F 125 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR F 137 " --> pdb=" O GLU I 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU I 69 " --> pdb=" O THR F 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN F 139 " --> pdb=" O THR I 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR I 67 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP F 141 " --> pdb=" O THR I 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR I 65 " --> pdb=" O TRP F 141 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 74 through 75 Processing sheet with id=AC7, first strand: chain 'G' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL G 123 " --> pdb=" O SER G 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER G 140 " --> pdb=" O VAL G 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL G 125 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR G 137 " --> pdb=" O GLU J 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU J 69 " --> pdb=" O THR G 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN G 139 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR J 67 " --> pdb=" O GLN G 139 " (cutoff:3.500A) removed outlier: 15.522A pdb=" N TRP G 141 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR J 65 " --> pdb=" O TRP G 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN J 63 " --> pdb=" O THR J 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER J 52 " --> pdb=" O GLU J 69 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL G 123 " --> pdb=" O SER G 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER G 140 " --> pdb=" O VAL G 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL G 125 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR G 137 " --> pdb=" O GLU J 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU J 69 " --> pdb=" O THR G 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN G 139 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR J 67 " --> pdb=" O GLN G 139 " (cutoff:3.500A) removed outlier: 15.522A pdb=" N TRP G 141 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR J 65 " --> pdb=" O TRP G 141 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 74 through 75 Processing sheet with id=AD1, first strand: chain 'H' and resid 79 through 82 removed outlier: 6.461A pdb=" N VAL H 123 " --> pdb=" O SER H 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER H 140 " --> pdb=" O VAL H 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL H 125 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR H 137 " --> pdb=" O GLU K 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU K 69 " --> pdb=" O THR H 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN H 139 " --> pdb=" O THR K 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR K 67 " --> pdb=" O GLN H 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP H 141 " --> pdb=" O THR K 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR K 65 " --> pdb=" O TRP H 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN K 63 " --> pdb=" O THR K 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER K 52 " --> pdb=" O GLU K 69 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 79 through 82 removed outlier: 6.461A pdb=" N VAL H 123 " --> pdb=" O SER H 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER H 140 " --> pdb=" O VAL H 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL H 125 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR H 137 " --> pdb=" O GLU K 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU K 69 " --> pdb=" O THR H 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN H 139 " --> pdb=" O THR K 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR K 67 " --> pdb=" O GLN H 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP H 141 " --> pdb=" O THR K 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR K 65 " --> pdb=" O TRP H 141 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 74 through 75 Processing sheet with id=AD4, first strand: chain 'J' and resid 74 through 75 Processing sheet with id=AD5, first strand: chain 'J' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL J 123 " --> pdb=" O SER J 140 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER J 140 " --> pdb=" O VAL J 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL J 125 " --> pdb=" O LEU J 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR J 137 " --> pdb=" O GLU L 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU L 69 " --> pdb=" O THR J 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN J 139 " --> pdb=" O THR L 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR L 67 " --> pdb=" O GLN J 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP J 141 " --> pdb=" O THR L 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR L 65 " --> pdb=" O TRP J 141 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN L 63 " --> pdb=" O THR L 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER L 52 " --> pdb=" O GLU L 69 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL J 123 " --> pdb=" O SER J 140 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER J 140 " --> pdb=" O VAL J 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL J 125 " --> pdb=" O LEU J 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR J 137 " --> pdb=" O GLU L 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU L 69 " --> pdb=" O THR J 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN J 139 " --> pdb=" O THR L 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR L 67 " --> pdb=" O GLN J 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP J 141 " --> pdb=" O THR L 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR L 65 " --> pdb=" O TRP J 141 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 74 through 75 Processing sheet with id=AD8, first strand: chain 'K' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL K 123 " --> pdb=" O SER K 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER K 140 " --> pdb=" O VAL K 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL K 125 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR K 137 " --> pdb=" O GLU M 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU M 69 " --> pdb=" O THR K 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN K 139 " --> pdb=" O THR M 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR M 67 " --> pdb=" O GLN K 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP K 141 " --> pdb=" O THR M 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR M 65 " --> pdb=" O TRP K 141 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN M 63 " --> pdb=" O THR M 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER M 52 " --> pdb=" O GLU M 69 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL K 123 " --> pdb=" O SER K 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER K 140 " --> pdb=" O VAL K 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL K 125 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR K 137 " --> pdb=" O GLU M 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU M 69 " --> pdb=" O THR K 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN K 139 " --> pdb=" O THR M 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR M 67 " --> pdb=" O GLN K 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP K 141 " --> pdb=" O THR M 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR M 65 " --> pdb=" O TRP K 141 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 74 through 75 Processing sheet with id=AE2, first strand: chain 'L' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL L 123 " --> pdb=" O SER L 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER L 140 " --> pdb=" O VAL L 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL L 125 " --> pdb=" O LEU L 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR L 137 " --> pdb=" O GLU O 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU O 69 " --> pdb=" O THR L 137 " (cutoff:3.500A) removed outlier: 13.550A pdb=" N GLN L 139 " --> pdb=" O THR O 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR O 67 " --> pdb=" O GLN L 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP L 141 " --> pdb=" O THR O 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR O 65 " --> pdb=" O TRP L 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN O 63 " --> pdb=" O THR O 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER O 52 " --> pdb=" O GLU O 69 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL L 123 " --> pdb=" O SER L 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER L 140 " --> pdb=" O VAL L 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL L 125 " --> pdb=" O LEU L 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR L 137 " --> pdb=" O GLU O 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU O 69 " --> pdb=" O THR L 137 " (cutoff:3.500A) removed outlier: 13.550A pdb=" N GLN L 139 " --> pdb=" O THR O 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR O 67 " --> pdb=" O GLN L 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP L 141 " --> pdb=" O THR O 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR O 65 " --> pdb=" O TRP L 141 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 74 through 75 Processing sheet with id=AE5, first strand: chain 'M' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL M 123 " --> pdb=" O SER M 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER M 140 " --> pdb=" O VAL M 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL M 125 " --> pdb=" O LEU M 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR M 137 " --> pdb=" O GLU P 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU P 69 " --> pdb=" O THR M 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN M 139 " --> pdb=" O THR P 67 " (cutoff:3.500A) removed outlier: 14.234A pdb=" N THR P 67 " --> pdb=" O GLN M 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP M 141 " --> pdb=" O THR P 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR P 65 " --> pdb=" O TRP M 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN P 63 " --> pdb=" O THR P 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER P 52 " --> pdb=" O GLU P 69 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL M 123 " --> pdb=" O SER M 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER M 140 " --> pdb=" O VAL M 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL M 125 " --> pdb=" O LEU M 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR M 137 " --> pdb=" O GLU P 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU P 69 " --> pdb=" O THR M 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN M 139 " --> pdb=" O THR P 67 " (cutoff:3.500A) removed outlier: 14.234A pdb=" N THR P 67 " --> pdb=" O GLN M 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP M 141 " --> pdb=" O THR P 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR P 65 " --> pdb=" O TRP M 141 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 74 through 75 Processing sheet with id=AE8, first strand: chain 'N' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL N 123 " --> pdb=" O SER N 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER N 140 " --> pdb=" O VAL N 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL N 125 " --> pdb=" O LEU N 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR N 137 " --> pdb=" O GLU Q 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU Q 69 " --> pdb=" O THR N 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN N 139 " --> pdb=" O THR Q 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR Q 67 " --> pdb=" O GLN N 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP N 141 " --> pdb=" O THR Q 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR Q 65 " --> pdb=" O TRP N 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN Q 63 " --> pdb=" O THR Q 58 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER Q 52 " --> pdb=" O GLU Q 69 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL N 123 " --> pdb=" O SER N 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER N 140 " --> pdb=" O VAL N 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL N 125 " --> pdb=" O LEU N 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR N 137 " --> pdb=" O GLU Q 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU Q 69 " --> pdb=" O THR N 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN N 139 " --> pdb=" O THR Q 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR Q 67 " --> pdb=" O GLN N 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP N 141 " --> pdb=" O THR Q 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR Q 65 " --> pdb=" O TRP N 141 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 74 through 75 Processing sheet with id=AF2, first strand: chain 'O' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL O 123 " --> pdb=" O SER O 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER O 140 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL O 125 " --> pdb=" O LEU O 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR O 137 " --> pdb=" O GLU R 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU R 69 " --> pdb=" O THR O 137 " (cutoff:3.500A) removed outlier: 13.550A pdb=" N GLN O 139 " --> pdb=" O THR R 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR R 67 " --> pdb=" O GLN O 139 " (cutoff:3.500A) removed outlier: 15.520A pdb=" N TRP O 141 " --> pdb=" O THR R 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR R 65 " --> pdb=" O TRP O 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN R 63 " --> pdb=" O THR R 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER R 52 " --> pdb=" O GLU R 69 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL O 123 " --> pdb=" O SER O 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER O 140 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL O 125 " --> pdb=" O LEU O 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR O 137 " --> pdb=" O GLU R 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU R 69 " --> pdb=" O THR O 137 " (cutoff:3.500A) removed outlier: 13.550A pdb=" N GLN O 139 " --> pdb=" O THR R 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR R 67 " --> pdb=" O GLN O 139 " (cutoff:3.500A) removed outlier: 15.520A pdb=" N TRP O 141 " --> pdb=" O THR R 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR R 65 " --> pdb=" O TRP O 141 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'P' and resid 74 through 75 Processing sheet with id=AF5, first strand: chain 'P' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL P 123 " --> pdb=" O SER P 140 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER P 140 " --> pdb=" O VAL P 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL P 125 " --> pdb=" O LEU P 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR P 137 " --> pdb=" O GLU S 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU S 69 " --> pdb=" O THR P 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN P 139 " --> pdb=" O THR S 67 " (cutoff:3.500A) removed outlier: 14.234A pdb=" N THR S 67 " --> pdb=" O GLN P 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP P 141 " --> pdb=" O THR S 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR S 65 " --> pdb=" O TRP P 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN S 63 " --> pdb=" O THR S 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER S 52 " --> pdb=" O GLU S 69 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL P 123 " --> pdb=" O SER P 140 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER P 140 " --> pdb=" O VAL P 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL P 125 " --> pdb=" O LEU P 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR P 137 " --> pdb=" O GLU S 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU S 69 " --> pdb=" O THR P 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN P 139 " --> pdb=" O THR S 67 " (cutoff:3.500A) removed outlier: 14.234A pdb=" N THR S 67 " --> pdb=" O GLN P 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP P 141 " --> pdb=" O THR S 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR S 65 " --> pdb=" O TRP P 141 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Q' and resid 74 through 75 Processing sheet with id=AF8, first strand: chain 'Q' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL Q 123 " --> pdb=" O SER Q 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER Q 140 " --> pdb=" O VAL Q 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL Q 125 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR Q 137 " --> pdb=" O GLU T 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU T 69 " --> pdb=" O THR Q 137 " (cutoff:3.500A) removed outlier: 13.548A pdb=" N GLN Q 139 " --> pdb=" O THR T 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR T 67 " --> pdb=" O GLN Q 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP Q 141 " --> pdb=" O THR T 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR T 65 " --> pdb=" O TRP Q 141 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN T 63 " --> pdb=" O THR T 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER T 52 " --> pdb=" O GLU T 69 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL Q 123 " --> pdb=" O SER Q 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER Q 140 " --> pdb=" O VAL Q 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL Q 125 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR Q 137 " --> pdb=" O GLU T 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU T 69 " --> pdb=" O THR Q 137 " (cutoff:3.500A) removed outlier: 13.548A pdb=" N GLN Q 139 " --> pdb=" O THR T 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR T 67 " --> pdb=" O GLN Q 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP Q 141 " --> pdb=" O THR T 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR T 65 " --> pdb=" O TRP Q 141 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'R' and resid 74 through 75 Processing sheet with id=AG2, first strand: chain 'R' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL R 123 " --> pdb=" O SER R 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER R 140 " --> pdb=" O VAL R 123 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL R 125 " --> pdb=" O LEU R 138 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 74 through 75 Processing sheet with id=AG4, first strand: chain 'S' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL S 123 " --> pdb=" O SER S 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER S 140 " --> pdb=" O VAL S 123 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL S 125 " --> pdb=" O LEU S 138 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'T' and resid 74 through 75 Processing sheet with id=AG6, first strand: chain 'T' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL T 123 " --> pdb=" O SER T 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER T 140 " --> pdb=" O VAL T 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL T 125 " --> pdb=" O LEU T 138 " (cutoff:3.500A) 1065 hydrogen bonds defined for protein. 3135 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: 6.84 Time building geometry restraints manager: 7.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6260 1.34 - 1.46: 3763 1.46 - 1.57: 9217 1.57 - 1.69: 0 1.69 - 1.80: 40 Bond restraints: 19280 Sorted by residual: bond pdb=" CG1 ILE K 33 " pdb=" CD1 ILE K 33 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.28e+00 bond pdb=" CG1 ILE M 33 " pdb=" CD1 ILE M 33 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.27e+00 bond pdb=" CG1 ILE H 33 " pdb=" CD1 ILE H 33 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.26e+00 bond pdb=" CG1 ILE E 33 " pdb=" CD1 ILE E 33 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.25e+00 bond pdb=" CG1 ILE P 33 " pdb=" CD1 ILE P 33 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.25e+00 ... (remaining 19275 not shown) Histogram of bond angle deviations from ideal: 101.80 - 108.24: 649 108.24 - 114.69: 11749 114.69 - 121.14: 8122 121.14 - 127.59: 5740 127.59 - 134.03: 160 Bond angle restraints: 26420 Sorted by residual: angle pdb=" N GLU M 46 " pdb=" CA GLU M 46 " pdb=" C GLU M 46 " ideal model delta sigma weight residual 110.91 114.58 -3.67 1.17e+00 7.31e-01 9.85e+00 angle pdb=" N GLU R 46 " pdb=" CA GLU R 46 " pdb=" C GLU R 46 " ideal model delta sigma weight residual 110.91 114.57 -3.66 1.17e+00 7.31e-01 9.78e+00 angle pdb=" N GLU I 46 " pdb=" CA GLU I 46 " pdb=" C GLU I 46 " ideal model delta sigma weight residual 110.91 114.56 -3.65 1.17e+00 7.31e-01 9.74e+00 angle pdb=" N GLU Q 46 " pdb=" CA GLU Q 46 " pdb=" C GLU Q 46 " ideal model delta sigma weight residual 110.91 114.56 -3.65 1.17e+00 7.31e-01 9.72e+00 angle pdb=" N GLU H 46 " pdb=" CA GLU H 46 " pdb=" C GLU H 46 " ideal model delta sigma weight residual 110.91 114.56 -3.65 1.17e+00 7.31e-01 9.71e+00 ... (remaining 26415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.68: 9840 12.68 - 25.37: 780 25.37 - 38.05: 280 38.05 - 50.73: 100 50.73 - 63.42: 20 Dihedral angle restraints: 11020 sinusoidal: 3620 harmonic: 7400 Sorted by residual: dihedral pdb=" CA GLY G 97 " pdb=" C GLY G 97 " pdb=" N SER G 98 " pdb=" CA SER G 98 " ideal model delta harmonic sigma weight residual -180.00 -162.61 -17.39 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA GLY F 97 " pdb=" C GLY F 97 " pdb=" N SER F 98 " pdb=" CA SER F 98 " ideal model delta harmonic sigma weight residual -180.00 -162.63 -17.37 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA GLY D 97 " pdb=" C GLY D 97 " pdb=" N SER D 98 " pdb=" CA SER D 98 " ideal model delta harmonic sigma weight residual -180.00 -162.63 -17.37 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 11017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1739 0.028 - 0.056: 1006 0.056 - 0.084: 349 0.084 - 0.112: 126 0.112 - 0.140: 100 Chirality restraints: 3320 Sorted by residual: chirality pdb=" CA SER C 14 " pdb=" N SER C 14 " pdb=" C SER C 14 " pdb=" CB SER C 14 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA SER E 14 " pdb=" N SER E 14 " pdb=" C SER E 14 " pdb=" CB SER E 14 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA SER I 14 " pdb=" N SER I 14 " pdb=" C SER I 14 " pdb=" CB SER I 14 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 3317 not shown) Planarity restraints: 3360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 33 " 0.007 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" C ILE C 33 " -0.023 2.00e-02 2.50e+03 pdb=" O ILE C 33 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY C 34 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 33 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" C ILE R 33 " 0.023 2.00e-02 2.50e+03 pdb=" O ILE R 33 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY R 34 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE O 33 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.73e+00 pdb=" C ILE O 33 " 0.023 2.00e-02 2.50e+03 pdb=" O ILE O 33 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY O 34 " -0.008 2.00e-02 2.50e+03 ... (remaining 3357 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 7417 2.89 - 3.39: 16953 3.39 - 3.90: 30518 3.90 - 4.40: 35604 4.40 - 4.90: 60971 Nonbonded interactions: 151463 Sorted by model distance: nonbonded pdb=" O VAL R 44 " pdb=" OG SER R 45 " model vdw 2.391 2.440 nonbonded pdb=" O VAL F 44 " pdb=" OG SER F 45 " model vdw 2.392 2.440 nonbonded pdb=" O VAL S 44 " pdb=" OG SER S 45 " model vdw 2.392 2.440 nonbonded pdb=" O VAL I 44 " pdb=" OG SER I 45 " model vdw 2.392 2.440 nonbonded pdb=" O VAL H 44 " pdb=" OG SER H 45 " model vdw 2.392 2.440 ... (remaining 151458 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.720 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 52.860 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 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 : 0.004 0.059 19280 Z= 0.280 Angle : 0.621 5.383 26420 Z= 0.369 Chirality : 0.044 0.140 3320 Planarity : 0.003 0.027 3360 Dihedral : 11.786 63.417 6300 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.16), residues: 2620 helix: 3.65 (0.15), residues: 600 sheet: 1.16 (0.17), residues: 1000 loop : -0.86 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 92 HIS 0.001 0.000 HIS T 68 PHE 0.008 0.001 PHE R 55 TYR 0.005 0.001 TYR D 143 ARG 0.000 0.000 ARG N 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 382 time to evaluate : 2.255 Fit side-chains REVERT: C 50 GLN cc_start: 0.8543 (mt0) cc_final: 0.8309 (mt0) REVERT: C 90 LYS cc_start: 0.8808 (mtmt) cc_final: 0.8543 (mtmt) REVERT: D 40 LEU cc_start: 0.8692 (tt) cc_final: 0.8440 (tp) REVERT: D 116 SER cc_start: 0.8724 (p) cc_final: 0.8374 (m) REVERT: D 130 ASP cc_start: 0.7967 (m-30) cc_final: 0.7714 (m-30) REVERT: F 33 ILE cc_start: 0.8440 (mt) cc_final: 0.8203 (tp) REVERT: F 40 LEU cc_start: 0.8378 (tt) cc_final: 0.8136 (tp) REVERT: F 59 ASN cc_start: 0.8877 (t0) cc_final: 0.7943 (t0) REVERT: G 59 ASN cc_start: 0.8913 (t0) cc_final: 0.8376 (t0) REVERT: G 130 ASP cc_start: 0.7888 (m-30) cc_final: 0.7682 (m-30) REVERT: H 22 MET cc_start: 0.8432 (mmp) cc_final: 0.8041 (mmp) REVERT: H 33 ILE cc_start: 0.8602 (mt) cc_final: 0.8382 (tp) REVERT: H 59 ASN cc_start: 0.8898 (t0) cc_final: 0.8650 (t0) REVERT: H 88 ASP cc_start: 0.8051 (t70) cc_final: 0.7737 (t70) REVERT: I 25 ILE cc_start: 0.8651 (mt) cc_final: 0.8386 (mm) REVERT: I 75 ASP cc_start: 0.8109 (t0) cc_final: 0.7782 (t0) REVERT: J 56 ASP cc_start: 0.8224 (t70) cc_final: 0.7961 (t70) REVERT: J 94 ASP cc_start: 0.7851 (m-30) cc_final: 0.7508 (m-30) REVERT: K 121 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8372 (mt-10) REVERT: M 94 ASP cc_start: 0.8019 (m-30) cc_final: 0.7628 (m-30) REVERT: M 130 ASP cc_start: 0.7970 (m-30) cc_final: 0.7671 (m-30) REVERT: N 130 ASP cc_start: 0.8159 (m-30) cc_final: 0.7887 (m-30) REVERT: P 50 GLN cc_start: 0.8631 (mt0) cc_final: 0.8328 (mt0) REVERT: P 56 ASP cc_start: 0.8055 (t70) cc_final: 0.7826 (t70) REVERT: Q 50 GLN cc_start: 0.8578 (mt0) cc_final: 0.8330 (mt0) REVERT: Q 56 ASP cc_start: 0.8022 (t70) cc_final: 0.7779 (t70) REVERT: Q 59 ASN cc_start: 0.8924 (t0) cc_final: 0.8512 (t0) REVERT: S 54 ASP cc_start: 0.8114 (t70) cc_final: 0.7873 (t0) REVERT: S 130 ASP cc_start: 0.7737 (m-30) cc_final: 0.7434 (m-30) REVERT: T 94 ASP cc_start: 0.8128 (m-30) cc_final: 0.7792 (m-30) REVERT: T 121 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8288 (mt-10) outliers start: 0 outliers final: 0 residues processed: 382 average time/residue: 0.8944 time to fit residues: 400.7359 Evaluate side-chains 307 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 203 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 236 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN E 50 GLN G 50 GLN I 50 GLN J 50 GLN L 50 GLN N 50 GLN P 50 GLN S 50 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19280 Z= 0.161 Angle : 0.463 7.491 26420 Z= 0.257 Chirality : 0.042 0.142 3320 Planarity : 0.002 0.021 3360 Dihedral : 4.611 15.450 2700 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.78 % Allowed : 3.94 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.16), residues: 2620 helix: 3.21 (0.18), residues: 700 sheet: 1.35 (0.17), residues: 1000 loop : -1.04 (0.16), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 141 HIS 0.003 0.002 HIS Q 68 PHE 0.009 0.001 PHE K 55 TYR 0.005 0.001 TYR M 143 ARG 0.001 0.000 ARG P 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 313 time to evaluate : 2.140 Fit side-chains REVERT: D 116 SER cc_start: 0.8669 (p) cc_final: 0.8274 (m) REVERT: E 94 ASP cc_start: 0.7461 (m-30) cc_final: 0.6887 (m-30) REVERT: E 101 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7268 (tp30) REVERT: F 56 ASP cc_start: 0.8106 (t0) cc_final: 0.7808 (t70) REVERT: F 59 ASN cc_start: 0.8840 (t0) cc_final: 0.8532 (t0) REVERT: F 60 THR cc_start: 0.9012 (m) cc_final: 0.8810 (m) REVERT: G 59 ASN cc_start: 0.8857 (t0) cc_final: 0.8346 (t0) REVERT: H 59 ASN cc_start: 0.8859 (t0) cc_final: 0.8638 (t0) REVERT: H 101 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7477 (mt-10) REVERT: I 25 ILE cc_start: 0.8723 (mt) cc_final: 0.8407 (mm) REVERT: K 121 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8314 (mt-10) REVERT: M 130 ASP cc_start: 0.7820 (m-30) cc_final: 0.7547 (m-30) REVERT: N 130 ASP cc_start: 0.8135 (m-30) cc_final: 0.7875 (m-30) REVERT: O 90 LYS cc_start: 0.8670 (mtpt) cc_final: 0.8430 (mtpt) REVERT: P 50 GLN cc_start: 0.8515 (mt0) cc_final: 0.8252 (mt0) REVERT: P 56 ASP cc_start: 0.7982 (t70) cc_final: 0.7707 (t70) REVERT: Q 50 GLN cc_start: 0.8489 (mt0) cc_final: 0.8246 (mt0) REVERT: Q 59 ASN cc_start: 0.8977 (t0) cc_final: 0.8546 (t0) REVERT: S 101 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7091 (tp30) REVERT: S 130 ASP cc_start: 0.7655 (m-30) cc_final: 0.7338 (m-30) REVERT: T 121 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8280 (mt-10) outliers start: 17 outliers final: 10 residues processed: 318 average time/residue: 0.9934 time to fit residues: 365.4531 Evaluate side-chains 295 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 283 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 101 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 196 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 236 optimal weight: 0.6980 chunk 255 optimal weight: 0.9990 chunk 210 optimal weight: 2.9990 chunk 234 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 189 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN D 50 GLN E 50 GLN F 50 GLN L 50 GLN N 50 GLN S 50 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19280 Z= 0.224 Angle : 0.501 6.568 26420 Z= 0.278 Chirality : 0.044 0.152 3320 Planarity : 0.003 0.022 3360 Dihedral : 4.862 16.084 2700 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.19 % Allowed : 6.33 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.16), residues: 2620 helix: 2.84 (0.18), residues: 720 sheet: 1.33 (0.17), residues: 1000 loop : -1.15 (0.16), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP T 92 HIS 0.006 0.003 HIS E 68 PHE 0.014 0.002 PHE K 55 TYR 0.007 0.001 TYR M 143 ARG 0.003 0.000 ARG P 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 291 time to evaluate : 2.062 Fit side-chains REVERT: B 50 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8309 (mt0) REVERT: D 116 SER cc_start: 0.8762 (p) cc_final: 0.8333 (m) REVERT: E 94 ASP cc_start: 0.7582 (m-30) cc_final: 0.7021 (m-30) REVERT: F 56 ASP cc_start: 0.8147 (t0) cc_final: 0.7874 (t70) REVERT: F 59 ASN cc_start: 0.8929 (t0) cc_final: 0.8615 (t0) REVERT: G 59 ASN cc_start: 0.8865 (t0) cc_final: 0.8410 (t0) REVERT: H 50 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8495 (mt0) REVERT: H 101 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7554 (mt-10) REVERT: H 143 TYR cc_start: 0.8420 (t80) cc_final: 0.8078 (t80) REVERT: I 25 ILE cc_start: 0.8723 (mt) cc_final: 0.8437 (mm) REVERT: I 101 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7205 (mm-30) REVERT: M 130 ASP cc_start: 0.7828 (m-30) cc_final: 0.7538 (m-30) REVERT: N 130 ASP cc_start: 0.8168 (m-30) cc_final: 0.7901 (m-30) REVERT: O 90 LYS cc_start: 0.8704 (mtpt) cc_final: 0.8481 (mtpt) REVERT: P 59 ASN cc_start: 0.8943 (t0) cc_final: 0.8462 (t0) REVERT: P 69 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7693 (mt-10) REVERT: P 77 ASP cc_start: 0.8424 (m-30) cc_final: 0.8173 (m-30) REVERT: Q 50 GLN cc_start: 0.8526 (mt0) cc_final: 0.8288 (mt0) REVERT: Q 59 ASN cc_start: 0.8911 (t0) cc_final: 0.8511 (t0) REVERT: R 94 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7397 (t0) REVERT: R 101 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7169 (mm-30) REVERT: S 101 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7171 (tp30) REVERT: S 130 ASP cc_start: 0.7836 (m-30) cc_final: 0.7488 (m-30) REVERT: T 101 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7307 (mt-10) outliers start: 26 outliers final: 14 residues processed: 301 average time/residue: 1.0145 time to fit residues: 351.6220 Evaluate side-chains 292 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 270 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain J residue 101 GLU Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain T residue 101 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 63.0431 > 50: distance: 15 - 22: 3.007 distance: 40 - 54: 6.875 distance: 52 - 54: 9.545 distance: 54 - 55: 7.474 distance: 55 - 58: 3.226 distance: 56 - 57: 6.269 distance: 56 - 62: 12.715 distance: 58 - 59: 3.113 distance: 59 - 61: 3.017 distance: 62 - 63: 21.927 distance: 63 - 64: 9.489 distance: 63 - 66: 12.811 distance: 64 - 65: 29.425 distance: 64 - 71: 10.265 distance: 66 - 67: 14.827 distance: 67 - 68: 10.387 distance: 68 - 69: 4.527 distance: 68 - 70: 8.837 distance: 71 - 72: 10.082 distance: 72 - 73: 17.440 distance: 72 - 75: 9.336 distance: 73 - 74: 14.777 distance: 73 - 78: 23.923 distance: 75 - 76: 19.917 distance: 75 - 77: 10.519 distance: 78 - 79: 24.177 distance: 79 - 80: 36.413 distance: 80 - 81: 22.250 distance: 80 - 84: 10.423 distance: 82 - 83: 6.785 distance: 84 - 85: 11.156 distance: 85 - 86: 12.093 distance: 85 - 88: 8.870 distance: 86 - 87: 23.453 distance: 86 - 93: 13.685 distance: 88 - 89: 10.079 distance: 89 - 90: 5.971 distance: 90 - 91: 4.318 distance: 93 - 94: 19.950 distance: 94 - 95: 6.030 distance: 94 - 97: 18.471 distance: 95 - 96: 30.128 distance: 95 - 100: 25.520 distance: 97 - 98: 13.675 distance: 97 - 99: 23.844 distance: 100 - 101: 20.107 distance: 101 - 102: 10.624 distance: 101 - 104: 34.166 distance: 102 - 103: 11.538 distance: 102 - 106: 40.054 distance: 104 - 105: 30.416 distance: 106 - 107: 8.794 distance: 106 - 112: 49.881 distance: 107 - 108: 16.624 distance: 107 - 110: 12.026 distance: 108 - 109: 31.061 distance: 108 - 113: 18.060 distance: 110 - 111: 57.144 distance: 111 - 112: 35.076 distance: 113 - 114: 19.839 distance: 114 - 115: 22.279 distance: 114 - 117: 20.916 distance: 115 - 116: 23.390 distance: 115 - 122: 13.850 distance: 117 - 118: 43.691 distance: 118 - 119: 13.944 distance: 119 - 120: 25.365 distance: 119 - 121: 9.939 distance: 122 - 123: 7.342 distance: 123 - 124: 26.373 distance: 123 - 126: 9.459 distance: 124 - 125: 16.721 distance: 124 - 127: 12.322