Starting phenix.real_space_refine on Mon Aug 5 02:27:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umn_26606/08_2024/7umn_26606_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umn_26606/08_2024/7umn_26606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umn_26606/08_2024/7umn_26606.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umn_26606/08_2024/7umn_26606.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umn_26606/08_2024/7umn_26606_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umn_26606/08_2024/7umn_26606_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 57 5.16 5 C 7845 2.51 5 N 2073 2.21 5 O 2400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 78": "OE1" <-> "OE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C GLU 116": "OE1" <-> "OE2" Residue "C GLU 144": "OE1" <-> "OE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "I GLU 10": "OE1" <-> "OE2" Residue "J GLU 10": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 12375 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2392 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 19, 'TRANS': 281} Chain breaks: 1 Chain: "B" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2392 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 19, 'TRANS': 281} Chain breaks: 1 Chain: "C" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2392 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 19, 'TRANS': 281} Chain breaks: 1 Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 938 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "I" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 938 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "J" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 938 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "L" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 795 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "M" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 795 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "N" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 795 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Time building chain proxies: 7.00, per 1000 atoms: 0.57 Number of scatterers: 12375 At special positions: 0 Unit cell: (110.55, 113.85, 119.625, 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 57 16.00 O 2400 8.00 N 2073 7.00 C 7845 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS B 59 " - pdb=" SG CYS B 71 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 306 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 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: 4.38 Conformation dependent library (CDL) restraints added in 2.1 seconds 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2904 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 36 sheets defined 14.0% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.686A pdb=" N GLU A 78 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 removed outlier: 3.856A pdb=" N GLU A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 140 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 574 through 592 Processing helix chain 'B' and resid 60 through 67 Processing helix chain 'B' and resid 74 through 78 removed outlier: 3.686A pdb=" N GLU B 78 " --> pdb=" O ILE B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 112 removed outlier: 3.856A pdb=" N GLU B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 571 through 573 No H-bonds generated for 'chain 'B' and resid 571 through 573' Processing helix chain 'B' and resid 574 through 592 Processing helix chain 'C' and resid 60 through 67 Processing helix chain 'C' and resid 74 through 78 removed outlier: 3.686A pdb=" N GLU C 78 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 112 removed outlier: 3.856A pdb=" N GLU C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL C 112 " --> pdb=" O GLN C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 140 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'C' and resid 571 through 573 No H-bonds generated for 'chain 'C' and resid 571 through 573' Processing helix chain 'C' and resid 574 through 592 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.613A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.614A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.613A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'M' and resid 29 through 31 No H-bonds generated for 'chain 'M' and resid 29 through 31' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.755A pdb=" N LEU A 54 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE A 83 " --> pdb=" O ILE A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 117 through 118 removed outlier: 7.891A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA5, first strand: chain 'A' and resid 167 through 169 Processing sheet with id=AA6, first strand: chain 'A' and resid 287 through 289 removed outlier: 3.906A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 295 through 296 Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 55 removed outlier: 6.756A pdb=" N LEU B 54 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE B 83 " --> pdb=" O ILE B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 117 through 118 removed outlier: 7.891A pdb=" N LEU B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AB2, first strand: chain 'B' and resid 130 through 131 Processing sheet with id=AB3, first strand: chain 'B' and resid 167 through 169 Processing sheet with id=AB4, first strand: chain 'B' and resid 287 through 289 removed outlier: 3.905A pdb=" N CYS B 282 " --> pdb=" O ILE B 289 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 295 through 296 Processing sheet with id=AB6, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.755A pdb=" N LEU C 54 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE C 83 " --> pdb=" O ILE C 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 117 through 118 removed outlier: 7.891A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 117 through 118 Processing sheet with id=AB9, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC1, first strand: chain 'C' and resid 167 through 169 Processing sheet with id=AC2, first strand: chain 'C' and resid 287 through 289 removed outlier: 3.906A pdb=" N CYS C 282 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 295 through 296 Processing sheet with id=AC4, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AC5, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.063A pdb=" N ASN H 33 " --> pdb=" O TRP H 99 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN H 52 " --> pdb=" O ILE H 57 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE H 57 " --> pdb=" O ASN H 52 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.385A pdb=" N VAL H 111 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AC8, first strand: chain 'I' and resid 10 through 12 removed outlier: 4.063A pdb=" N ASN I 33 " --> pdb=" O TRP I 99 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N MET I 34 " --> pdb=" O ILE I 50 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN I 52 " --> pdb=" O ILE I 57 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE I 57 " --> pdb=" O ASN I 52 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 10 through 12 removed outlier: 4.385A pdb=" N VAL I 111 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AD2, first strand: chain 'J' and resid 10 through 12 removed outlier: 4.063A pdb=" N ASN J 33 " --> pdb=" O TRP J 99 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N MET J 34 " --> pdb=" O ILE J 50 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN J 52 " --> pdb=" O ILE J 57 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE J 57 " --> pdb=" O ASN J 52 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 10 through 12 removed outlier: 4.385A pdb=" N VAL J 111 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.738A pdb=" N GLU L 17 " --> pdb=" O THR L 77 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR L 77 " --> pdb=" O GLU L 17 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.817A pdb=" N CYS L 88 " --> pdb=" O GLY L 99 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY L 101 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N TYR L 86 " --> pdb=" O GLY L 101 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP L 35 " --> pdb=" O TRP L 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 4 through 7 removed outlier: 5.738A pdb=" N GLU M 17 " --> pdb=" O THR M 77 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR M 77 " --> pdb=" O GLU M 17 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 10 through 11 removed outlier: 3.817A pdb=" N CYS M 88 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY M 101 " --> pdb=" O TYR M 86 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TYR M 86 " --> pdb=" O GLY M 101 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP M 35 " --> pdb=" O TRP M 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 4 through 7 removed outlier: 5.737A pdb=" N GLU N 17 " --> pdb=" O THR N 77 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR N 77 " --> pdb=" O GLU N 17 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.817A pdb=" N CYS N 88 " --> pdb=" O GLY N 99 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY N 101 " --> pdb=" O TYR N 86 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N TYR N 86 " --> pdb=" O GLY N 101 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP N 35 " --> pdb=" O TRP N 47 " (cutoff:3.500A) 435 hydrogen bonds defined for protein. 1053 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: 3.89 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3948 1.34 - 1.46: 3422 1.46 - 1.59: 5257 1.59 - 1.71: 0 1.71 - 1.83: 78 Bond restraints: 12705 Sorted by residual: bond pdb=" N MET B 577 " pdb=" CA MET B 577 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.23e-02 6.61e+03 1.34e+01 bond pdb=" N MET C 577 " pdb=" CA MET C 577 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.23e-02 6.61e+03 1.34e+01 bond pdb=" N MET A 577 " pdb=" CA MET A 577 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.23e-02 6.61e+03 1.31e+01 bond pdb=" C MET B 577 " pdb=" O MET B 577 " ideal model delta sigma weight residual 1.237 1.279 -0.042 1.19e-02 7.06e+03 1.24e+01 bond pdb=" C MET C 577 " pdb=" O MET C 577 " ideal model delta sigma weight residual 1.237 1.278 -0.042 1.19e-02 7.06e+03 1.22e+01 ... (remaining 12700 not shown) Histogram of bond angle deviations from ideal: 97.06 - 104.48: 238 104.48 - 111.90: 5852 111.90 - 119.32: 4324 119.32 - 126.74: 6614 126.74 - 134.16: 228 Bond angle restraints: 17256 Sorted by residual: angle pdb=" C PHE A 115 " pdb=" CA PHE A 115 " pdb=" CB PHE A 115 " ideal model delta sigma weight residual 112.43 106.10 6.33 1.91e+00 2.74e-01 1.10e+01 angle pdb=" C PHE B 115 " pdb=" CA PHE B 115 " pdb=" CB PHE B 115 " ideal model delta sigma weight residual 112.43 106.10 6.33 1.91e+00 2.74e-01 1.10e+01 angle pdb=" C PHE C 115 " pdb=" CA PHE C 115 " pdb=" CB PHE C 115 " ideal model delta sigma weight residual 112.43 106.11 6.32 1.91e+00 2.74e-01 1.09e+01 angle pdb=" CA GLN L 37 " pdb=" CB GLN L 37 " pdb=" CG GLN L 37 " ideal model delta sigma weight residual 114.10 120.56 -6.46 2.00e+00 2.50e-01 1.04e+01 angle pdb=" CA GLN N 37 " pdb=" CB GLN N 37 " pdb=" CG GLN N 37 " ideal model delta sigma weight residual 114.10 120.56 -6.46 2.00e+00 2.50e-01 1.04e+01 ... (remaining 17251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.85: 6724 14.85 - 29.70: 638 29.70 - 44.55: 132 44.55 - 59.40: 21 59.40 - 74.25: 15 Dihedral angle restraints: 7530 sinusoidal: 2955 harmonic: 4575 Sorted by residual: dihedral pdb=" CA PHE B 115 " pdb=" C PHE B 115 " pdb=" N GLU B 116 " pdb=" CA GLU B 116 " ideal model delta harmonic sigma weight residual 180.00 151.38 28.62 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA PHE C 115 " pdb=" C PHE C 115 " pdb=" N GLU C 116 " pdb=" CA GLU C 116 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA PHE A 115 " pdb=" C PHE A 115 " pdb=" N GLU A 116 " pdb=" CA GLU A 116 " ideal model delta harmonic sigma weight residual 180.00 151.41 28.59 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 7527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1630 0.089 - 0.177: 191 0.177 - 0.266: 0 0.266 - 0.354: 0 0.354 - 0.443: 3 Chirality restraints: 1824 Sorted by residual: chirality pdb=" CG LEU A 45 " pdb=" CB LEU A 45 " pdb=" CD1 LEU A 45 " pdb=" CD2 LEU A 45 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.91e+00 chirality pdb=" CG LEU C 45 " pdb=" CB LEU C 45 " pdb=" CD1 LEU C 45 " pdb=" CD2 LEU C 45 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.90e+00 chirality pdb=" CG LEU B 45 " pdb=" CB LEU B 45 " pdb=" CD1 LEU B 45 " pdb=" CD2 LEU B 45 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.86e+00 ... (remaining 1821 not shown) Planarity restraints: 2217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 299 " 0.059 5.00e-02 4.00e+02 8.89e-02 1.26e+01 pdb=" N PRO B 300 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO B 300 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 300 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 299 " 0.059 5.00e-02 4.00e+02 8.88e-02 1.26e+01 pdb=" N PRO C 300 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO C 300 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 300 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 299 " 0.059 5.00e-02 4.00e+02 8.88e-02 1.26e+01 pdb=" N PRO A 300 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 300 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 300 " 0.049 5.00e-02 4.00e+02 ... (remaining 2214 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1832 2.74 - 3.28: 13049 3.28 - 3.82: 20267 3.82 - 4.36: 25796 4.36 - 4.90: 44560 Nonbonded interactions: 105504 Sorted by model distance: nonbonded pdb=" ND2 ASN A 187 " pdb=" OD1 ASP H 31 " model vdw 2.206 3.120 nonbonded pdb=" ND2 ASN B 187 " pdb=" OD1 ASP I 31 " model vdw 2.206 3.120 nonbonded pdb=" ND2 ASN C 187 " pdb=" OD1 ASP J 31 " model vdw 2.206 3.120 nonbonded pdb=" OG SER H 102 " pdb=" OH TYR H 108 " model vdw 2.249 3.040 nonbonded pdb=" OG SER I 102 " pdb=" OH TYR I 108 " model vdw 2.249 3.040 ... (remaining 105499 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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 group one per residue 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: 1.190 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: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 34.520 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 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 0.074 12705 Z= 0.751 Angle : 0.893 7.416 17256 Z= 0.499 Chirality : 0.056 0.443 1824 Planarity : 0.007 0.089 2217 Dihedral : 12.513 74.250 4572 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.22 % Allowed : 0.22 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.19), residues: 1557 helix: -3.07 (0.34), residues: 132 sheet: -0.46 (0.25), residues: 432 loop : -2.00 (0.17), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP J 99 HIS 0.007 0.003 HIS C 98 PHE 0.055 0.005 PHE B 588 TYR 0.048 0.004 TYR H 107 ARG 0.007 0.001 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 205 time to evaluate : 1.322 Fit side-chains REVERT: A 56 LEU cc_start: 0.7289 (mt) cc_final: 0.7043 (mt) REVERT: A 158 ASN cc_start: 0.8785 (m-40) cc_final: 0.8570 (m-40) REVERT: B 158 ASN cc_start: 0.8763 (m-40) cc_final: 0.8546 (m-40) REVERT: B 197 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8451 (p) REVERT: B 248 ASN cc_start: 0.7604 (t0) cc_final: 0.7312 (t0) REVERT: H 65 LYS cc_start: 0.7247 (tptt) cc_final: 0.7046 (tptp) REVERT: I 34 MET cc_start: 0.7105 (mmm) cc_final: 0.6622 (mpp) REVERT: I 82 GLN cc_start: 0.7298 (tp40) cc_final: 0.6929 (tp40) REVERT: J 6 GLN cc_start: 0.7531 (mt0) cc_final: 0.6921 (mt0) REVERT: J 82 GLN cc_start: 0.7281 (tp40) cc_final: 0.6962 (tp40) REVERT: L 21 MET cc_start: 0.6347 (ptp) cc_final: 0.6057 (ptt) REVERT: L 89 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7725 (tm-30) REVERT: M 21 MET cc_start: 0.6370 (ptp) cc_final: 0.6133 (ptt) outliers start: 3 outliers final: 0 residues processed: 205 average time/residue: 0.2555 time to fit residues: 76.5173 Evaluate side-chains 143 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 208 HIS N 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12705 Z= 0.231 Angle : 0.704 9.827 17256 Z= 0.358 Chirality : 0.046 0.161 1824 Planarity : 0.005 0.064 2217 Dihedral : 6.165 27.402 1720 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.55 % Allowed : 6.64 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.60 (0.20), residues: 1557 helix: -1.30 (0.39), residues: 156 sheet: -0.19 (0.26), residues: 447 loop : -1.50 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 47 HIS 0.003 0.001 HIS L 34 PHE 0.019 0.002 PHE A 588 TYR 0.023 0.002 TYR I 107 ARG 0.005 0.001 ARG I 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 202 time to evaluate : 1.293 Fit side-chains REVERT: C 82 TYR cc_start: 0.7534 (p90) cc_final: 0.7251 (p90) REVERT: I 82 GLN cc_start: 0.7195 (tp40) cc_final: 0.6741 (tp40) REVERT: J 51 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.8013 (tp) outliers start: 21 outliers final: 10 residues processed: 211 average time/residue: 0.2078 time to fit residues: 65.9417 Evaluate side-chains 177 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 166 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 150 optimal weight: 20.0000 chunk 123 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 ASN B 581 ASN C 581 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 12705 Z= 0.477 Angle : 0.792 10.153 17256 Z= 0.406 Chirality : 0.050 0.163 1824 Planarity : 0.006 0.061 2217 Dihedral : 6.302 27.296 1719 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.88 % Allowed : 11.95 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.67 (0.21), residues: 1557 helix: -1.67 (0.38), residues: 159 sheet: -0.11 (0.26), residues: 453 loop : -1.57 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP J 47 HIS 0.005 0.002 HIS N 34 PHE 0.030 0.003 PHE B 115 TYR 0.021 0.002 TYR J 107 ARG 0.005 0.001 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 177 time to evaluate : 1.339 Fit side-chains REVERT: B 248 ASN cc_start: 0.7810 (t0) cc_final: 0.7568 (t0) REVERT: C 82 TYR cc_start: 0.7788 (p90) cc_final: 0.7498 (p90) REVERT: J 98 ARG cc_start: 0.7833 (ttp80) cc_final: 0.7062 (ttp80) outliers start: 39 outliers final: 25 residues processed: 204 average time/residue: 0.2018 time to fit residues: 62.4281 Evaluate side-chains 185 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 160 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 98 PHE Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN B 55 GLN C 581 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12705 Z= 0.236 Angle : 0.655 9.824 17256 Z= 0.334 Chirality : 0.046 0.155 1824 Planarity : 0.004 0.050 2217 Dihedral : 5.655 25.169 1719 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.14 % Allowed : 13.50 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.35 (0.21), residues: 1557 helix: -1.42 (0.38), residues: 159 sheet: 0.08 (0.26), residues: 456 loop : -1.34 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 99 HIS 0.006 0.001 HIS M 34 PHE 0.025 0.002 PHE B 115 TYR 0.022 0.002 TYR A 82 ARG 0.002 0.000 ARG B 229 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 181 time to evaluate : 1.444 Fit side-chains REVERT: A 187 ASN cc_start: 0.7996 (p0) cc_final: 0.7645 (p0) REVERT: A 590 ASP cc_start: 0.5771 (m-30) cc_final: 0.5307 (m-30) REVERT: I 51 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8183 (tp) REVERT: I 98 ARG cc_start: 0.7855 (ttp-110) cc_final: 0.7384 (ttp-110) outliers start: 29 outliers final: 16 residues processed: 199 average time/residue: 0.2025 time to fit residues: 61.5391 Evaluate side-chains 183 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 166 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 98 PHE Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.4883 > 50: distance: 16 - 20: 10.343 distance: 20 - 21: 12.906 distance: 21 - 22: 4.444 distance: 22 - 23: 6.268 distance: 22 - 24: 16.094 distance: 24 - 25: 8.247 distance: 25 - 26: 14.213 distance: 26 - 27: 9.923 distance: 26 - 32: 21.909 distance: 28 - 29: 5.736 distance: 28 - 30: 11.414 distance: 29 - 31: 7.366 distance: 32 - 33: 18.207 distance: 33 - 34: 38.563 distance: 33 - 36: 39.721 distance: 34 - 35: 12.055 distance: 34 - 37: 14.414 distance: 37 - 38: 4.258 distance: 37 - 43: 19.302 distance: 38 - 39: 21.953 distance: 38 - 41: 23.478 distance: 39 - 40: 26.060 distance: 39 - 44: 13.485 distance: 41 - 42: 33.322 distance: 42 - 43: 32.798 distance: 44 - 45: 11.362 distance: 45 - 46: 17.853 distance: 45 - 48: 20.488 distance: 46 - 47: 10.165 distance: 46 - 52: 10.823 distance: 48 - 49: 15.883 distance: 49 - 50: 13.792 distance: 49 - 51: 6.468 distance: 52 - 53: 10.606 distance: 53 - 54: 16.688 distance: 53 - 56: 14.711 distance: 54 - 55: 9.062 distance: 54 - 61: 17.543 distance: 56 - 57: 7.474 distance: 57 - 58: 6.005 distance: 58 - 59: 4.637 distance: 58 - 60: 12.667 distance: 61 - 62: 20.699 distance: 62 - 63: 19.220 distance: 62 - 65: 14.555 distance: 63 - 64: 5.240 distance: 63 - 69: 32.599 distance: 65 - 66: 28.858 distance: 66 - 67: 11.965 distance: 66 - 68: 6.694 distance: 69 - 70: 11.802 distance: 70 - 71: 12.520 distance: 71 - 72: 34.491 distance: 71 - 73: 9.276 distance: 73 - 74: 26.602 distance: 74 - 75: 17.339 distance: 74 - 77: 10.173 distance: 75 - 76: 27.455 distance: 75 - 81: 14.561 distance: 77 - 78: 11.536 distance: 78 - 79: 32.732 distance: 78 - 80: 9.098 distance: 81 - 82: 21.576 distance: 82 - 83: 13.186 distance: 82 - 85: 42.796 distance: 83 - 84: 22.167 distance: 83 - 87: 16.338 distance: 85 - 86: 27.020 distance: 86 - 115: 8.430