Starting phenix.real_space_refine on Sat Mar 16 20:08:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk5_27483/03_2024/8dk5_27483.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk5_27483/03_2024/8dk5_27483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk5_27483/03_2024/8dk5_27483.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk5_27483/03_2024/8dk5_27483.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk5_27483/03_2024/8dk5_27483.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk5_27483/03_2024/8dk5_27483.pdb" } resolution = 2.71 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= 0.005 sd= 0.114 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 298 5.49 5 S 32 5.16 5 C 8911 2.51 5 N 2816 2.21 5 O 3561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "H GLU 77": "OE1" <-> "OE2" Residue "K GLU 175": "OE1" <-> "OE2" Residue "N GLU 68": "OE1" <-> "OE2" Residue "N GLU 84": "OE1" <-> "OE2" Residue "N GLU 104": "OE1" <-> "OE2" Residue "N GLU 175": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15618 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 736 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 736 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1759 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "I" Number of atoms: 3088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3088 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Chain: "J" Number of atoms: 3021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3021 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Time building chain proxies: 8.22, per 1000 atoms: 0.53 Number of scatterers: 15618 At special positions: 0 Unit cell: (138.336, 124.608, 121.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 298 15.00 O 3561 8.00 N 2816 7.00 C 8911 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS K 44 " - pdb=" SG CYS K 118 " distance=2.03 Simple disulfide: pdb=" SG CYS K 181 " - pdb=" SG CYS K 246 " distance=2.03 Simple disulfide: pdb=" SG CYS N 44 " - pdb=" SG CYS N 118 " distance=2.03 Simple disulfide: pdb=" SG CYS N 181 " - pdb=" SG CYS N 246 " distance=2.03 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: 6.82 Conformation dependent library (CDL) restraints added in 1.7 seconds 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2250 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 21 sheets defined 46.9% alpha, 19.8% beta 123 base pairs and 282 stacking pairs defined. Time for finding SS restraints: 6.56 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.591A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.804A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.645A pdb=" N LEU C 55 " --> pdb=" O MET C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.547A pdb=" N LEU C 116 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 50 removed outlier: 3.609A pdb=" N TYR D 43 " --> pdb=" O SER D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.531A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.746A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.510A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.620A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 56 through 85 removed outlier: 3.548A pdb=" N ASN H 85 " --> pdb=" O LEU H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 125 Processing helix chain 'K' and resid 50 through 52 No H-bonds generated for 'chain 'K' and resid 50 through 52' Processing helix chain 'K' and resid 109 through 113 removed outlier: 4.114A pdb=" N SER K 113 " --> pdb=" O SER K 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 52 No H-bonds generated for 'chain 'N' and resid 50 through 52' Processing helix chain 'N' and resid 84 through 87 removed outlier: 3.828A pdb=" N LYS N 87 " --> pdb=" O GLU N 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 84 through 87' Processing helix chain 'N' and resid 109 through 113 removed outlier: 3.674A pdb=" N ASP N 112 " --> pdb=" O THR N 109 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER N 113 " --> pdb=" O SER N 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 109 through 113' Processing helix chain 'N' and resid 237 through 241 removed outlier: 3.708A pdb=" N ASP N 240 " --> pdb=" O GLU N 237 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR N 241 " --> pdb=" O SER N 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 237 through 241' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.970A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.573A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.155A pdb=" N ARG C 42 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.501A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.139A pdb=" N ARG G 42 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 25 through 28 removed outlier: 3.564A pdb=" N VAL K 101 " --> pdb=" O CYS K 44 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 32 through 34 removed outlier: 7.998A pdb=" N TYR K 54 " --> pdb=" O TYR K 74 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TYR K 74 " --> pdb=" O TYR K 54 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE K 56 " --> pdb=" O TYR K 72 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR K 72 " --> pdb=" O ILE K 56 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP K 58 " --> pdb=" O ILE K 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 168 through 171 removed outlier: 3.501A pdb=" N MET K 169 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU K 263 " --> pdb=" O MET K 169 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA K 171 " --> pdb=" O GLU K 263 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU K 191 " --> pdb=" O TYR K 207 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N TYR K 207 " --> pdb=" O LEU K 191 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TRP K 193 " --> pdb=" O LEU K 205 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 168 through 171 removed outlier: 3.501A pdb=" N MET K 169 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU K 263 " --> pdb=" O MET K 169 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA K 171 " --> pdb=" O GLU K 263 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR K 255 " --> pdb=" O GLN K 248 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 177 through 180 Processing sheet with id=AB7, first strand: chain 'N' and resid 25 through 27 Processing sheet with id=AB8, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.274A pdb=" N LYS N 60 " --> pdb=" O TRP N 69 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TRP N 69 " --> pdb=" O LYS N 60 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR N 62 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU N 67 " --> pdb=" O THR N 62 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 32 through 34 removed outlier: 4.029A pdb=" N TYR N 131 " --> pdb=" O ARG N 120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 39 through 43 Processing sheet with id=AC2, first strand: chain 'N' and resid 162 through 164 removed outlier: 3.956A pdb=" N PHE N 229 " --> pdb=" O CYS N 181 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP N 228 " --> pdb=" O SER N 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 168 through 171 removed outlier: 6.816A pdb=" N LEU N 191 " --> pdb=" O TYR N 207 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TYR N 207 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TRP N 193 " --> pdb=" O LEU N 205 " (cutoff:3.500A) 543 hydrogen bonds defined for protein. 1530 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 296 hydrogen bonds 592 hydrogen bond angles 0 basepair planarities 123 basepair parallelities 282 stacking parallelities Total time for adding SS restraints: 5.73 Time building geometry restraints manager: 7.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 15 1.20 - 1.36: 4547 1.36 - 1.52: 7263 1.52 - 1.67: 4647 1.67 - 1.83: 53 Bond restraints: 16525 Sorted by residual: bond pdb=" C LEU B 90 " pdb=" O LEU B 90 " ideal model delta sigma weight residual 1.237 1.052 0.184 1.19e-02 7.06e+03 2.40e+02 bond pdb=" O3' DG I 92 " pdb=" P DA I 93 " ideal model delta sigma weight residual 1.607 1.382 0.225 1.50e-02 4.44e+03 2.24e+02 bond pdb=" C MET C 51 " pdb=" O MET C 51 " ideal model delta sigma weight residual 1.236 1.045 0.191 1.29e-02 6.01e+03 2.20e+02 bond pdb=" C LEU C 93 " pdb=" O LEU C 93 " ideal model delta sigma weight residual 1.237 1.069 0.168 1.17e-02 7.31e+03 2.06e+02 bond pdb=" O3' DG I 110 " pdb=" P DC I 111 " ideal model delta sigma weight residual 1.607 1.393 0.214 1.50e-02 4.44e+03 2.04e+02 ... (remaining 16520 not shown) Histogram of bond angle deviations from ideal: 82.92 - 93.73: 6 93.73 - 104.53: 1240 104.53 - 115.34: 10893 115.34 - 126.15: 10446 126.15 - 136.96: 1029 Bond angle restraints: 23614 Sorted by residual: angle pdb=" N SER H 33 " pdb=" CA SER H 33 " pdb=" C SER H 33 " ideal model delta sigma weight residual 110.61 126.96 -16.35 1.25e+00 6.40e-01 1.71e+02 angle pdb=" O3' DA J 94 " pdb=" C3' DA J 94 " pdb=" C2' DA J 94 " ideal model delta sigma weight residual 111.50 126.85 -15.35 1.50e+00 4.44e-01 1.05e+02 angle pdb=" CB MET C 51 " pdb=" CG MET C 51 " pdb=" SD MET C 51 " ideal model delta sigma weight residual 112.70 82.92 29.78 3.00e+00 1.11e-01 9.85e+01 angle pdb=" C3' DG I 60 " pdb=" O3' DG I 60 " pdb=" P DA I 61 " ideal model delta sigma weight residual 120.20 132.96 -12.76 1.50e+00 4.44e-01 7.24e+01 angle pdb=" C3' DT J 76 " pdb=" O3' DT J 76 " pdb=" P DT J 77 " ideal model delta sigma weight residual 120.20 132.68 -12.48 1.50e+00 4.44e-01 6.92e+01 ... (remaining 23609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.07: 7383 32.07 - 64.14: 1797 64.14 - 96.21: 54 96.21 - 128.28: 1 128.28 - 160.35: 3 Dihedral angle restraints: 9238 sinusoidal: 5726 harmonic: 3512 Sorted by residual: dihedral pdb=" C LEU E 82 " pdb=" N LEU E 82 " pdb=" CA LEU E 82 " pdb=" CB LEU E 82 " ideal model delta harmonic sigma weight residual -122.60 -108.52 -14.08 0 2.50e+00 1.60e-01 3.17e+01 dihedral pdb=" C SER H 33 " pdb=" N SER H 33 " pdb=" CA SER H 33 " pdb=" CB SER H 33 " ideal model delta harmonic sigma weight residual -122.60 -134.49 11.89 0 2.50e+00 1.60e-01 2.26e+01 dihedral pdb=" CA PRO D 104 " pdb=" C PRO D 104 " pdb=" N GLY D 105 " pdb=" CA GLY D 105 " ideal model delta harmonic sigma weight residual -180.00 -156.75 -23.25 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 9235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 2570 0.137 - 0.275: 66 0.275 - 0.412: 16 0.412 - 0.550: 8 0.550 - 0.687: 3 Chirality restraints: 2663 Sorted by residual: chirality pdb=" CA SER H 33 " pdb=" N SER H 33 " pdb=" C SER H 33 " pdb=" CB SER H 33 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" CG LEU C 93 " pdb=" CB LEU C 93 " pdb=" CD1 LEU C 93 " pdb=" CD2 LEU C 93 " both_signs ideal model delta sigma weight residual False -2.59 -1.94 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" P DA I 93 " pdb=" OP1 DA I 93 " pdb=" OP2 DA I 93 " pdb=" O5' DA I 93 " both_signs ideal model delta sigma weight residual True 2.35 -1.79 0.55 2.00e-01 2.50e+01 7.70e+00 ... (remaining 2660 not shown) Planarity restraints: 1949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA J 36 " 0.080 2.00e-02 2.50e+03 6.68e-02 1.23e+02 pdb=" N9 DA J 36 " -0.051 2.00e-02 2.50e+03 pdb=" C8 DA J 36 " 0.033 2.00e-02 2.50e+03 pdb=" N7 DA J 36 " 0.021 2.00e-02 2.50e+03 pdb=" C5 DA J 36 " 0.009 2.00e-02 2.50e+03 pdb=" C6 DA J 36 " -0.084 2.00e-02 2.50e+03 pdb=" N6 DA J 36 " 0.053 2.00e-02 2.50e+03 pdb=" N1 DA J 36 " 0.020 2.00e-02 2.50e+03 pdb=" C2 DA J 36 " 0.082 2.00e-02 2.50e+03 pdb=" N3 DA J 36 " -0.017 2.00e-02 2.50e+03 pdb=" C4 DA J 36 " -0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 92 " -0.035 2.00e-02 2.50e+03 7.33e-02 5.37e+01 pdb=" C GLU C 92 " 0.127 2.00e-02 2.50e+03 pdb=" O GLU C 92 " -0.049 2.00e-02 2.50e+03 pdb=" N LEU C 93 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 46 " -0.038 2.00e-02 2.50e+03 4.12e-02 4.66e+01 pdb=" N9 DA I 46 " -0.009 2.00e-02 2.50e+03 pdb=" C8 DA I 46 " -0.013 2.00e-02 2.50e+03 pdb=" N7 DA I 46 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 46 " 0.113 2.00e-02 2.50e+03 pdb=" C6 DA I 46 " -0.030 2.00e-02 2.50e+03 pdb=" N6 DA I 46 " -0.041 2.00e-02 2.50e+03 pdb=" N1 DA I 46 " -0.015 2.00e-02 2.50e+03 pdb=" C2 DA I 46 " 0.012 2.00e-02 2.50e+03 pdb=" N3 DA I 46 " -0.010 2.00e-02 2.50e+03 pdb=" C4 DA I 46 " 0.034 2.00e-02 2.50e+03 ... (remaining 1946 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 369 2.65 - 3.21: 12316 3.21 - 3.78: 27747 3.78 - 4.34: 39127 4.34 - 4.90: 56293 Nonbonded interactions: 135852 Sorted by model distance: nonbonded pdb=" O SER H 33 " pdb=" OG SER H 33 " model vdw 2.088 2.440 nonbonded pdb=" CA MET C 51 " pdb=" SD MET C 51 " model vdw 2.308 3.064 nonbonded pdb=" O MET C 51 " pdb=" CG MET C 51 " model vdw 2.318 3.440 nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.325 2.440 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.350 2.440 ... (remaining 135847 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 'E' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 118)) } ncs_group { reference = (chain 'D' and resid 32 through 125) selection = (chain 'H' and resid 32 through 125) } ncs_group { reference = chain 'K' selection = (chain 'N' and (resid 23 through 187 or (resid 188 and (name N or name CA or nam \ e C or name O or name CB )) or resid 189 through 264 or (resid 265 and (name N o \ r name CA or name C or name O or name CB )))) } 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: 0.760 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: 3.610 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 46.190 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 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:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 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 : 0.011 0.225 16525 Z= 0.613 Angle : 1.114 29.781 23614 Z= 0.625 Chirality : 0.065 0.687 2663 Planarity : 0.008 0.126 1949 Dihedral : 27.411 160.347 6976 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.55 % Favored : 95.28 % Rotamer: Outliers : 0.39 % Allowed : 21.94 % Favored : 77.67 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.22), residues: 1186 helix: -0.21 (0.19), residues: 537 sheet: -0.23 (0.34), residues: 234 loop : -1.27 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP N 58 HIS 0.006 0.002 HIS C 31 PHE 0.029 0.003 PHE A 78 TYR 0.045 0.002 TYR H 41 ARG 0.012 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 252 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.7855 (ttt180) cc_final: 0.7437 (tpt90) REVERT: A 133 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7319 (mt-10) REVERT: D 36 GLU cc_start: 0.7481 (pt0) cc_final: 0.7195 (pt0) REVERT: D 43 TYR cc_start: 0.7937 (t80) cc_final: 0.7572 (t80) REVERT: D 60 MET cc_start: 0.8470 (tpp) cc_final: 0.8267 (tpp) REVERT: D 84 TYR cc_start: 0.8471 (m-10) cc_final: 0.8263 (m-10) REVERT: D 87 ARG cc_start: 0.7790 (mtp85) cc_final: 0.7550 (mtt-85) REVERT: E 115 LYS cc_start: 0.8747 (mttt) cc_final: 0.8515 (mppt) REVERT: E 133 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7889 (mt-10) REVERT: F 79 LYS cc_start: 0.8287 (mttt) cc_final: 0.7933 (mttp) REVERT: H 72 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7111 (mt-10) REVERT: H 87 ARG cc_start: 0.7953 (mmt-90) cc_final: 0.7670 (mmt180) REVERT: K 42 MET cc_start: 0.8184 (mtt) cc_final: 0.7805 (mtt) REVERT: K 109 THR cc_start: 0.6745 (m) cc_final: 0.6463 (t) REVERT: K 261 LYS cc_start: 0.8368 (mttm) cc_final: 0.7978 (mtpm) REVERT: N 95 ASP cc_start: 0.7821 (t70) cc_final: 0.7548 (t0) REVERT: N 170 HIS cc_start: 0.7954 (m90) cc_final: 0.6579 (m90) REVERT: N 173 LEU cc_start: 0.8157 (mm) cc_final: 0.7856 (tm) REVERT: N 180 THR cc_start: 0.8870 (m) cc_final: 0.8351 (p) outliers start: 4 outliers final: 3 residues processed: 255 average time/residue: 1.6367 time to fit residues: 449.1677 Evaluate side-chains 163 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 160 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 159 ASP Chi-restraints excluded: chain N residue 186 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 129 optimal weight: 20.0000 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS B 25 ASN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN K 196 GLN ** N 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 227 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16525 Z= 0.199 Angle : 0.584 7.178 23614 Z= 0.342 Chirality : 0.036 0.174 2663 Planarity : 0.004 0.078 1949 Dihedral : 29.697 154.742 4684 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.82 % Allowed : 23.41 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.24), residues: 1186 helix: 1.46 (0.21), residues: 549 sheet: 0.10 (0.34), residues: 234 loop : -1.04 (0.28), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 58 HIS 0.004 0.001 HIS H 50 PHE 0.006 0.001 PHE E 67 TYR 0.022 0.001 TYR H 41 ARG 0.004 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 167 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.7932 (ttt180) cc_final: 0.7569 (tpt90) REVERT: A 133 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7228 (mt-10) REVERT: D 43 TYR cc_start: 0.7891 (t80) cc_final: 0.7533 (t80) REVERT: E 133 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7945 (mt-10) REVERT: G 73 ASN cc_start: 0.7650 (t0) cc_final: 0.7401 (t0) REVERT: G 91 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7005 (tt0) REVERT: H 72 GLU cc_start: 0.7352 (mt-10) cc_final: 0.7138 (mt-10) REVERT: H 87 ARG cc_start: 0.7859 (mmt-90) cc_final: 0.7574 (mmt180) REVERT: K 261 LYS cc_start: 0.8569 (mttm) cc_final: 0.8140 (mtpm) REVERT: N 137 SER cc_start: 0.7790 (OUTLIER) cc_final: 0.7526 (t) REVERT: N 180 THR cc_start: 0.8776 (m) cc_final: 0.8305 (p) outliers start: 39 outliers final: 13 residues processed: 190 average time/residue: 1.6831 time to fit residues: 344.6332 Evaluate side-chains 173 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 158 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 159 ASP Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 175 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 20.0000 chunk 40 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 104 optimal weight: 0.1980 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 112 GLN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 196 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 16525 Z= 0.363 Angle : 0.633 8.356 23614 Z= 0.365 Chirality : 0.039 0.180 2663 Planarity : 0.005 0.063 1949 Dihedral : 29.998 157.749 4681 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.70 % Allowed : 22.92 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.24), residues: 1186 helix: 1.64 (0.22), residues: 550 sheet: 0.18 (0.34), residues: 234 loop : -1.03 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP N 58 HIS 0.006 0.001 HIS N 249 PHE 0.009 0.002 PHE N 229 TYR 0.020 0.002 TYR H 41 ARG 0.005 0.001 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 166 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8073 (ttt180) cc_final: 0.7652 (tpt90) REVERT: B 31 LYS cc_start: 0.8493 (ttmt) cc_final: 0.7973 (tttm) REVERT: D 43 TYR cc_start: 0.7864 (t80) cc_final: 0.7640 (t80) REVERT: E 49 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.6611 (ptp90) REVERT: E 63 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7970 (mmt-90) REVERT: F 45 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7180 (mtm180) REVERT: G 91 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: H 87 ARG cc_start: 0.7980 (mmt-90) cc_final: 0.7627 (mmt90) REVERT: K 57 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8274 (mm110) REVERT: K 81 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8176 (ttpt) REVERT: K 103 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.5950 (tpt) REVERT: K 169 MET cc_start: 0.8123 (ppp) cc_final: 0.7876 (pmm) REVERT: K 258 SER cc_start: 0.8582 (m) cc_final: 0.8096 (p) REVERT: K 261 LYS cc_start: 0.8586 (mttm) cc_final: 0.8142 (mtpm) REVERT: N 25 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8224 (mm110) REVERT: N 165 SER cc_start: 0.7096 (OUTLIER) cc_final: 0.6840 (m) REVERT: N 180 THR cc_start: 0.8656 (m) cc_final: 0.8330 (p) outliers start: 48 outliers final: 19 residues processed: 188 average time/residue: 1.7730 time to fit residues: 357.8789 Evaluate side-chains 170 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 57 GLN Chi-restraints excluded: chain K residue 81 LYS Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 175 GLU Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 241 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 196 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16525 Z= 0.190 Angle : 0.553 7.498 23614 Z= 0.324 Chirality : 0.034 0.145 2663 Planarity : 0.004 0.052 1949 Dihedral : 29.545 155.131 4679 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.31 % Allowed : 24.78 % Favored : 70.91 % 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: 1.22 (0.24), residues: 1186 helix: 2.21 (0.22), residues: 550 sheet: 0.29 (0.35), residues: 234 loop : -0.85 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 69 HIS 0.004 0.001 HIS H 50 PHE 0.007 0.001 PHE N 229 TYR 0.016 0.001 TYR H 41 ARG 0.006 0.000 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 158 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8023 (ttt180) cc_final: 0.7684 (tpt90) REVERT: A 133 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7679 (mt-10) REVERT: B 31 LYS cc_start: 0.8471 (ttmt) cc_final: 0.7951 (tttm) REVERT: D 34 ARG cc_start: 0.7045 (ptm160) cc_final: 0.5350 (ptt180) REVERT: D 43 TYR cc_start: 0.7837 (t80) cc_final: 0.7520 (t80) REVERT: G 91 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7141 (tt0) REVERT: H 87 ARG cc_start: 0.7885 (mmt-90) cc_final: 0.7553 (mmt90) REVERT: K 161 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8624 (tptm) REVERT: K 261 LYS cc_start: 0.8539 (mttm) cc_final: 0.8016 (mtpm) REVERT: N 165 SER cc_start: 0.6733 (OUTLIER) cc_final: 0.6412 (m) REVERT: N 180 THR cc_start: 0.8711 (m) cc_final: 0.8423 (p) REVERT: N 263 GLU cc_start: 0.7260 (tm-30) cc_final: 0.7048 (tm-30) outliers start: 44 outliers final: 11 residues processed: 180 average time/residue: 1.7007 time to fit residues: 329.1466 Evaluate side-chains 158 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 144 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 159 ASP Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 175 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN C 24 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16525 Z= 0.260 Angle : 0.580 7.559 23614 Z= 0.337 Chirality : 0.036 0.151 2663 Planarity : 0.004 0.048 1949 Dihedral : 29.647 156.806 4679 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.21 % Allowed : 25.17 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.25), residues: 1186 helix: 2.24 (0.22), residues: 548 sheet: 0.63 (0.36), residues: 214 loop : -0.91 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 58 HIS 0.005 0.001 HIS H 50 PHE 0.009 0.001 PHE N 229 TYR 0.015 0.001 TYR N 72 ARG 0.006 0.000 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 156 time to evaluate : 1.316 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8062 (ttt180) cc_final: 0.7717 (tpt90) REVERT: B 31 LYS cc_start: 0.8492 (ttmt) cc_final: 0.7965 (tttm) REVERT: D 34 ARG cc_start: 0.7101 (ptm160) cc_final: 0.5431 (ptt180) REVERT: D 43 TYR cc_start: 0.7800 (t80) cc_final: 0.7505 (t80) REVERT: D 102 LEU cc_start: 0.8562 (mp) cc_final: 0.8302 (mp) REVERT: E 49 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.6665 (ptp90) REVERT: F 45 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7048 (mtm180) REVERT: G 91 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7209 (tt0) REVERT: H 87 ARG cc_start: 0.7939 (mmt-90) cc_final: 0.7597 (mmt90) REVERT: K 57 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8411 (mm110) REVERT: K 103 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.5902 (tpt) REVERT: K 258 SER cc_start: 0.8396 (m) cc_final: 0.7913 (p) REVERT: K 261 LYS cc_start: 0.8419 (mttm) cc_final: 0.8147 (mtpm) REVERT: N 68 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7399 (pt0) REVERT: N 165 SER cc_start: 0.7047 (OUTLIER) cc_final: 0.6784 (m) REVERT: N 180 THR cc_start: 0.8601 (m) cc_final: 0.8302 (p) outliers start: 43 outliers final: 18 residues processed: 176 average time/residue: 1.7523 time to fit residues: 331.2245 Evaluate side-chains 164 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 57 GLN Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 159 ASP Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 175 GLU Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 192 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16525 Z= 0.308 Angle : 0.600 8.545 23614 Z= 0.347 Chirality : 0.037 0.143 2663 Planarity : 0.004 0.044 1949 Dihedral : 29.749 157.197 4679 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.60 % Allowed : 25.17 % Favored : 70.23 % 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: 1.18 (0.24), residues: 1186 helix: 2.10 (0.22), residues: 548 sheet: 0.60 (0.36), residues: 214 loop : -0.91 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 58 HIS 0.005 0.001 HIS N 249 PHE 0.009 0.001 PHE N 229 TYR 0.017 0.002 TYR N 72 ARG 0.004 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 150 time to evaluate : 1.399 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8305 (tttm) REVERT: A 115 LYS cc_start: 0.8457 (mttt) cc_final: 0.8229 (mtmp) REVERT: A 129 ARG cc_start: 0.8085 (ttt180) cc_final: 0.7611 (tpt90) REVERT: B 31 LYS cc_start: 0.8511 (ttmt) cc_final: 0.7966 (tttm) REVERT: B 91 LYS cc_start: 0.8662 (ttmt) cc_final: 0.8417 (ttpp) REVERT: D 34 ARG cc_start: 0.7148 (ptm160) cc_final: 0.5506 (ptt180) REVERT: D 43 TYR cc_start: 0.7806 (t80) cc_final: 0.7562 (t80) REVERT: D 102 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8344 (mp) REVERT: E 49 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.6690 (ptp90) REVERT: E 63 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7934 (mmt-90) REVERT: E 129 ARG cc_start: 0.7946 (tmt170) cc_final: 0.7725 (tmt170) REVERT: F 45 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7066 (mtm180) REVERT: F 93 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7855 (mp10) REVERT: G 91 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7171 (tt0) REVERT: H 36 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7399 (mt-10) REVERT: H 87 ARG cc_start: 0.7982 (mmt-90) cc_final: 0.7727 (mmt90) REVERT: K 57 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8325 (mm110) REVERT: K 81 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8011 (ttpt) REVERT: K 103 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.5830 (tpt) REVERT: K 258 SER cc_start: 0.8448 (m) cc_final: 0.7959 (p) REVERT: K 261 LYS cc_start: 0.8582 (mttm) cc_final: 0.8155 (mtpm) REVERT: N 25 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7747 (mp10) REVERT: N 165 SER cc_start: 0.7179 (OUTLIER) cc_final: 0.6898 (m) REVERT: N 176 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7450 (ttm-80) REVERT: N 180 THR cc_start: 0.8627 (m) cc_final: 0.8353 (p) outliers start: 47 outliers final: 21 residues processed: 177 average time/residue: 1.7272 time to fit residues: 328.8032 Evaluate side-chains 174 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 140 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 57 GLN Chi-restraints excluded: chain K residue 81 LYS Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 129 LEU Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 175 GLU Chi-restraints excluded: chain N residue 176 ARG Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 241 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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: 53.8484 > 50: distance: 31 - 41: 3.002 distance: 76 - 77: 3.636 distance: 77 - 78: 3.896 distance: 77 - 80: 9.519 distance: 78 - 79: 8.680 distance: 78 - 83: 4.782 distance: 79 - 104: 7.867 distance: 80 - 81: 7.167 distance: 80 - 82: 3.994 distance: 83 - 84: 4.430 distance: 84 - 87: 4.246 distance: 85 - 86: 7.932 distance: 85 - 88: 8.034 distance: 86 - 111: 10.689 distance: 88 - 89: 4.868 distance: 89 - 90: 3.699 distance: 89 - 92: 7.541 distance: 90 - 91: 6.265 distance: 90 - 96: 5.907 distance: 91 - 118: 13.923 distance: 92 - 93: 4.327 distance: 93 - 94: 12.086 distance: 94 - 95: 6.433 distance: 96 - 97: 9.523 distance: 97 - 98: 8.365 distance: 97 - 100: 10.906 distance: 98 - 99: 8.745 distance: 98 - 104: 6.100 distance: 99 - 130: 6.265 distance: 100 - 101: 5.806 distance: 101 - 102: 10.650 distance: 101 - 103: 3.744 distance: 104 - 105: 10.913 distance: 105 - 106: 7.535 distance: 105 - 108: 17.099 distance: 106 - 107: 8.581 distance: 106 - 111: 6.503 distance: 107 - 135: 13.029 distance: 108 - 109: 13.903 distance: 108 - 110: 21.419 distance: 111 - 112: 7.746 distance: 112 - 115: 3.400 distance: 113 - 114: 8.568 distance: 114 - 143: 14.000 distance: 115 - 116: 12.351 distance: 115 - 117: 15.671 distance: 118 - 119: 6.206 distance: 119 - 120: 6.090 distance: 119 - 122: 4.890 distance: 120 - 130: 3.760 distance: 121 - 152: 10.367 distance: 122 - 123: 7.267 distance: 123 - 124: 4.838 distance: 123 - 125: 4.355 distance: 125 - 127: 4.972 distance: 126 - 128: 3.719 distance: 128 - 129: 5.288 distance: 130 - 131: 19.254 distance: 131 - 132: 17.748 distance: 131 - 134: 10.175 distance: 132 - 133: 15.406 distance: 132 - 135: 30.514 distance: 135 - 136: 15.108 distance: 136 - 137: 4.778 distance: 136 - 139: 11.482 distance: 137 - 138: 8.126 distance: 137 - 143: 18.365 distance: 139 - 140: 4.589 distance: 140 - 141: 15.893 distance: 140 - 142: 19.522 distance: 143 - 144: 6.558 distance: 144 - 145: 4.747 distance: 144 - 147: 3.927 distance: 145 - 146: 6.956 distance: 145 - 152: 4.530 distance: 147 - 148: 9.199 distance: 148 - 149: 12.000 distance: 149 - 150: 8.926 distance: 150 - 151: 21.801