Starting phenix.real_space_refine on Thu Feb 15 13:58:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umn_26606/02_2024/7umn_26606_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umn_26606/02_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_26606/02_2024/7umn_26606.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umn_26606/02_2024/7umn_26606.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umn_26606/02_2024/7umn_26606_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umn_26606/02_2024/7umn_26606_neut.pdb" } 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-5238/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: 6.66, per 1000 atoms: 0.54 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: 4.52 Conformation dependent library (CDL) restraints added in 2.4 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: 1.65 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: 3.75 Time building geometry restraints manager: 4.96 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 2.520 nonbonded pdb=" ND2 ASN B 187 " pdb=" OD1 ASP I 31 " model vdw 2.206 2.520 nonbonded pdb=" ND2 ASN C 187 " pdb=" OD1 ASP J 31 " model vdw 2.206 2.520 nonbonded pdb=" OG SER H 102 " pdb=" OH TYR H 108 " model vdw 2.249 2.440 nonbonded pdb=" OG SER I 102 " pdb=" OH TYR I 108 " model vdw 2.249 2.440 ... (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 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: 1.000 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: 4.290 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 34.470 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.630 ------------------------------------------------------------------------------- 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 : 1.497 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: 0.2368 time to fit residues: 70.9870 Evaluate side-chains 143 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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: 8.9990 chunk 115 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 39 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 208 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12705 Z= 0.193 Angle : 0.680 10.964 17256 Z= 0.342 Chirality : 0.046 0.160 1824 Planarity : 0.005 0.063 2217 Dihedral : 6.000 26.395 1720 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.40 % Allowed : 6.56 % Favored : 92.04 % 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: -1.56 (0.20), residues: 1557 helix: -1.35 (0.38), residues: 159 sheet: -0.21 (0.26), residues: 447 loop : -1.43 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 47 HIS 0.005 0.001 HIS M 34 PHE 0.020 0.002 PHE A 588 TYR 0.019 0.002 TYR I 107 ARG 0.005 0.001 ARG H 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 210 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 191 time to evaluate : 1.446 Fit side-chains revert: symmetry clash REVERT: A 82 TYR cc_start: 0.7370 (p90) cc_final: 0.7158 (p90) REVERT: B 158 ASN cc_start: 0.8614 (m-40) cc_final: 0.8393 (m-40) REVERT: B 590 ASP cc_start: 0.5592 (m-30) cc_final: 0.5176 (m-30) REVERT: C 82 TYR cc_start: 0.7292 (p90) cc_final: 0.7048 (p90) REVERT: J 82 GLN cc_start: 0.7263 (tp40) cc_final: 0.7014 (tp40) outliers start: 19 outliers final: 7 residues processed: 198 average time/residue: 0.2138 time to fit residues: 63.5846 Evaluate side-chains 161 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 154 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN 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 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: 3.9990 chunk 43 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 150 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 ASN C 42 ASN C 290 ASN C 581 ASN L 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 12705 Z= 0.397 Angle : 0.749 10.758 17256 Z= 0.382 Chirality : 0.049 0.164 1824 Planarity : 0.006 0.060 2217 Dihedral : 6.063 26.420 1719 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.80 % Allowed : 11.95 % Favored : 85.25 % 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: -1.56 (0.21), residues: 1557 helix: -1.58 (0.38), residues: 159 sheet: -0.11 (0.26), residues: 459 loop : -1.46 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 47 HIS 0.005 0.001 HIS M 34 PHE 0.028 0.003 PHE B 115 TYR 0.022 0.002 TYR J 107 ARG 0.003 0.001 ARG L 24 *********************** 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 212 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 174 time to evaluate : 1.400 Fit side-chains REVERT: B 197 THR cc_start: 0.8701 (p) cc_final: 0.8459 (t) REVERT: C 82 TYR cc_start: 0.7704 (p90) cc_final: 0.7464 (p90) REVERT: I 51 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8281 (tp) REVERT: I 82 GLN cc_start: 0.7443 (tp40) cc_final: 0.7119 (tp40) REVERT: J 51 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8377 (tp) REVERT: J 98 ARG cc_start: 0.7660 (ttp80) cc_final: 0.7366 (ttp-110) outliers start: 38 outliers final: 22 residues processed: 199 average time/residue: 0.2173 time to fit residues: 66.1020 Evaluate side-chains 184 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 160 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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 B residue 580 LEU 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 C residue 580 LEU Chi-restraints excluded: chain H residue 31 ASP 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 J residue 50 ILE Chi-restraints excluded: chain J residue 51 ILE 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 98 PHE Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 98 PHE 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: 0.9990 chunk 104 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 55 GLN A 290 ASN B 42 ASN B 55 GLN B 290 ASN C 55 GLN C 581 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12705 Z= 0.177 Angle : 0.624 10.816 17256 Z= 0.316 Chirality : 0.045 0.153 1824 Planarity : 0.004 0.049 2217 Dihedral : 5.422 24.517 1719 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.06 % Allowed : 14.01 % Favored : 83.92 % 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: -1.24 (0.21), residues: 1557 helix: -1.27 (0.38), residues: 159 sheet: 0.05 (0.26), residues: 456 loop : -1.21 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 112 HIS 0.006 0.001 HIS N 34 PHE 0.025 0.002 PHE B 115 TYR 0.020 0.001 TYR A 82 ARG 0.002 0.000 ARG I 98 *********************** 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 217 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 189 time to evaluate : 1.394 Fit side-chains revert: symmetry clash REVERT: I 51 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8171 (tp) REVERT: I 98 ARG cc_start: 0.7667 (ttp-110) cc_final: 0.7296 (ttp-110) REVERT: J 51 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8242 (tp) outliers start: 28 outliers final: 15 residues processed: 206 average time/residue: 0.2381 time to fit residues: 75.1324 Evaluate side-chains 179 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 162 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 580 LEU Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain H residue 31 ASP 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 J residue 50 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain L residue 53 ASN 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 0.8980 chunk 2 optimal weight: 0.0670 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 126 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 0 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 132 optimal weight: 50.0000 chunk 37 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN C 581 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12705 Z= 0.171 Angle : 0.604 10.780 17256 Z= 0.305 Chirality : 0.044 0.157 1824 Planarity : 0.004 0.049 2217 Dihedral : 5.207 22.557 1719 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.51 % Allowed : 15.27 % Favored : 82.23 % 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: -1.12 (0.21), residues: 1557 helix: -1.22 (0.39), residues: 156 sheet: 0.15 (0.25), residues: 456 loop : -1.13 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 47 HIS 0.005 0.001 HIS L 34 PHE 0.051 0.002 PHE C 588 TYR 0.021 0.001 TYR J 27 ARG 0.006 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 5 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 220 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 186 time to evaluate : 1.509 Fit side-chains revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8113 (mt) cc_final: 0.7754 (mt) REVERT: I 51 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.8095 (tp) REVERT: I 82 GLN cc_start: 0.7284 (tp40) cc_final: 0.6997 (tp40) REVERT: I 98 ARG cc_start: 0.7626 (ttp-110) cc_final: 0.7098 (ttp80) REVERT: J 51 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8139 (tp) outliers start: 34 outliers final: 18 residues processed: 210 average time/residue: 0.2100 time to fit residues: 67.1861 Evaluate side-chains 193 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 173 time to evaluate : 1.482 ------------------------------------------------------------------------------- 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 A residue 155 THR Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 115 PHE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 580 LEU 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 J residue 51 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 53 ASN 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 N residue 58 VAL Chi-restraints excluded: chain N residue 73 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 86 optimal weight: 0.0870 chunk 36 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 overall best weight: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 581 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12705 Z= 0.281 Angle : 0.652 11.222 17256 Z= 0.328 Chirality : 0.045 0.149 1824 Planarity : 0.004 0.047 2217 Dihedral : 5.323 22.275 1719 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.73 % Allowed : 15.63 % Favored : 81.64 % 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: -1.21 (0.21), residues: 1557 helix: -1.23 (0.39), residues: 156 sheet: -0.01 (0.24), residues: 501 loop : -1.19 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 47 HIS 0.005 0.001 HIS L 34 PHE 0.020 0.002 PHE A 115 TYR 0.021 0.002 TYR J 27 ARG 0.005 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 6 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 221 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 184 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 590 ASP cc_start: 0.5597 (m-30) cc_final: 0.5128 (m-30) REVERT: B 248 ASN cc_start: 0.7891 (t0) cc_final: 0.7638 (t0) REVERT: I 51 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8199 (tp) REVERT: J 51 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8276 (tp) outliers start: 37 outliers final: 25 residues processed: 207 average time/residue: 0.2058 time to fit residues: 65.4171 Evaluate side-chains 193 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 166 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 115 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 73 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 6.9990 chunk 84 optimal weight: 0.0370 chunk 108 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 overall best weight: 2.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12705 Z= 0.338 Angle : 0.695 11.110 17256 Z= 0.351 Chirality : 0.047 0.189 1824 Planarity : 0.005 0.050 2217 Dihedral : 5.517 21.561 1719 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.80 % Allowed : 16.81 % Favored : 80.38 % 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: -1.29 (0.21), residues: 1557 helix: -1.35 (0.39), residues: 156 sheet: -0.04 (0.24), residues: 498 loop : -1.25 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 47 HIS 0.005 0.001 HIS L 34 PHE 0.028 0.003 PHE C 588 TYR 0.020 0.002 TYR A 82 ARG 0.003 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 7 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: 38 poor density : 170 time to evaluate : 1.432 Fit side-chains revert: symmetry clash REVERT: A 590 ASP cc_start: 0.5723 (m-30) cc_final: 0.5276 (m-30) REVERT: B 248 ASN cc_start: 0.7848 (t0) cc_final: 0.7627 (t0) REVERT: I 51 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8238 (tp) REVERT: J 51 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8331 (tp) REVERT: M 11 MET cc_start: 0.3895 (ttt) cc_final: 0.3495 (ttt) outliers start: 38 outliers final: 32 residues processed: 191 average time/residue: 0.2096 time to fit residues: 60.9653 Evaluate side-chains 196 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 162 time to evaluate : 1.481 ------------------------------------------------------------------------------- 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 115 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 53 ASN 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 L residue 106 LEU Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 44 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN ** C 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12705 Z= 0.172 Angle : 0.611 10.501 17256 Z= 0.309 Chirality : 0.044 0.204 1824 Planarity : 0.004 0.044 2217 Dihedral : 5.130 20.633 1719 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.36 % Allowed : 17.70 % Favored : 79.94 % 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: -1.08 (0.21), residues: 1557 helix: -1.19 (0.38), residues: 156 sheet: 0.15 (0.24), residues: 492 loop : -1.13 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 47 HIS 0.006 0.001 HIS L 34 PHE 0.055 0.002 PHE B 588 TYR 0.019 0.001 TYR I 60 ARG 0.004 0.000 ARG N 24 *********************** REFINEMENT MACRO_CYCLE 8 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 222 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 190 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 286 GLN cc_start: 0.5407 (OUTLIER) cc_final: 0.4380 (mt0) REVERT: I 51 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8143 (tp) REVERT: I 98 ARG cc_start: 0.7644 (ttp-110) cc_final: 0.7131 (ttp80) outliers start: 32 outliers final: 21 residues processed: 208 average time/residue: 0.2165 time to fit residues: 67.3845 Evaluate side-chains 201 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 178 time to evaluate : 1.419 ------------------------------------------------------------------------------- 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 115 PHE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 286 GLN Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 53 ASN 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 48 ILE Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 0.6980 chunk 137 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 136 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 581 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12705 Z= 0.204 Angle : 0.629 9.975 17256 Z= 0.320 Chirality : 0.045 0.211 1824 Planarity : 0.004 0.072 2217 Dihedral : 5.120 21.544 1719 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.43 % Allowed : 17.92 % Favored : 79.65 % 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: -1.08 (0.21), residues: 1557 helix: -1.21 (0.38), residues: 156 sheet: 0.09 (0.24), residues: 498 loop : -1.10 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 47 HIS 0.005 0.001 HIS L 34 PHE 0.045 0.002 PHE A 588 TYR 0.018 0.001 TYR H 32 ARG 0.009 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 9 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 218 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 185 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 ASN cc_start: 0.7655 (t0) cc_final: 0.7424 (t0) REVERT: A 302 THR cc_start: 0.7700 (OUTLIER) cc_final: 0.7473 (m) REVERT: C 187 ASN cc_start: 0.7594 (p0) cc_final: 0.7392 (p0) REVERT: C 286 GLN cc_start: 0.5398 (OUTLIER) cc_final: 0.4344 (mt0) REVERT: I 51 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8146 (tp) REVERT: I 98 ARG cc_start: 0.7656 (ttp-110) cc_final: 0.7101 (ttp80) outliers start: 33 outliers final: 25 residues processed: 205 average time/residue: 0.2265 time to fit residues: 69.6604 Evaluate side-chains 205 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 177 time to evaluate : 1.447 ------------------------------------------------------------------------------- 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 A residue 155 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 115 PHE Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 286 GLN Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 53 ASN 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 48 ILE Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 68 optimal weight: 0.0170 chunk 101 optimal weight: 5.9990 chunk 152 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 chunk 74 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12705 Z= 0.180 Angle : 0.613 9.321 17256 Z= 0.314 Chirality : 0.045 0.235 1824 Planarity : 0.004 0.045 2217 Dihedral : 5.007 19.636 1719 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.99 % Allowed : 18.66 % Favored : 79.35 % 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: -1.00 (0.21), residues: 1557 helix: -1.23 (0.38), residues: 156 sheet: 0.22 (0.24), residues: 492 loop : -1.06 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 47 HIS 0.005 0.001 HIS L 34 PHE 0.048 0.002 PHE A 588 TYR 0.018 0.001 TYR H 27 ARG 0.006 0.000 ARG H 98 ********************** REFINEMENT MACRO_CYCLE 10 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 214 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 187 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 ASN cc_start: 0.7680 (t0) cc_final: 0.7442 (t0) REVERT: A 302 THR cc_start: 0.7653 (OUTLIER) cc_final: 0.7412 (m) REVERT: C 66 LEU cc_start: 0.8065 (mt) cc_final: 0.7662 (mt) REVERT: C 187 ASN cc_start: 0.7544 (p0) cc_final: 0.7330 (p0) REVERT: C 286 GLN cc_start: 0.5408 (OUTLIER) cc_final: 0.4402 (mt0) REVERT: I 51 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.8072 (tp) REVERT: I 98 ARG cc_start: 0.7559 (ttp-110) cc_final: 0.7072 (ttp80) outliers start: 27 outliers final: 22 residues processed: 202 average time/residue: 0.2110 time to fit residues: 64.5283 Evaluate side-chains 205 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 180 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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 A residue 155 THR Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 115 PHE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 286 GLN Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 53 ASN 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 48 ILE Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.151721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.129594 restraints weight = 18823.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.130058 restraints weight = 15605.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.130487 restraints weight = 13527.513| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 12705 Z= 0.489 Angle : 0.788 11.583 17256 Z= 0.405 Chirality : 0.050 0.219 1824 Planarity : 0.005 0.047 2217 Dihedral : 5.707 23.334 1719 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.21 % Allowed : 18.88 % Favored : 78.91 % 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: -1.49 (0.21), residues: 1557 helix: -1.74 (0.37), residues: 153 sheet: -0.21 (0.24), residues: 504 loop : -1.32 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP H 47 HIS 0.005 0.002 HIS A 183 PHE 0.057 0.004 PHE A 588 TYR 0.020 0.002 TYR A 82 ARG 0.005 0.001 ARG L 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2394.80 seconds wall clock time: 45 minutes 50.10 seconds (2750.10 seconds total)