Starting phenix.real_space_refine on Thu Feb 15 01:24:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lht_0897/02_2024/6lht_0897_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lht_0897/02_2024/6lht_0897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lht_0897/02_2024/6lht_0897.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lht_0897/02_2024/6lht_0897.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lht_0897/02_2024/6lht_0897_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lht_0897/02_2024/6lht_0897_updated.pdb" } resolution = 3.67 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= -0.025 sd= 1.249 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 69 5.16 5 C 6916 2.51 5 N 1800 2.21 5 O 1969 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 67": "NH1" <-> "NH2" Residue "L GLU 87": "OE1" <-> "OE2" Residue "L TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "A ARG 130": "NH1" <-> "NH2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A ARG 250": "NH1" <-> "NH2" Residue "A ARG 291": "NH1" <-> "NH2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C GLU 124": "OE1" <-> "OE2" Residue "C ARG 130": "NH1" <-> "NH2" Residue "C GLU 134": "OE1" <-> "OE2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C ARG 250": "NH1" <-> "NH2" Residue "C ARG 291": "NH1" <-> "NH2" Residue "D ARG 120": "NH1" <-> "NH2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D ARG 130": "NH1" <-> "NH2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D ARG 166": "NH1" <-> "NH2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D ARG 291": "NH1" <-> "NH2" Residue "E ARG 120": "NH1" <-> "NH2" Residue "E GLU 124": "OE1" <-> "OE2" Residue "E ARG 130": "NH1" <-> "NH2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "E ARG 250": "NH1" <-> "NH2" Residue "E ARG 291": "NH1" <-> "NH2" Residue "B ARG 120": "NH1" <-> "NH2" Residue "B GLU 124": "OE1" <-> "OE2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B ARG 166": "NH1" <-> "NH2" Residue "B ARG 250": "NH1" <-> "NH2" Residue "B ARG 291": "NH1" <-> "NH2" 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: 10754 Number of models: 1 Model: "" Number of chains: 12 Chain: "L" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 888 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "H" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 943 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "A" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1754 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 19, 'TRANS': 198} Chain breaks: 1 Chain: "C" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1754 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 19, 'TRANS': 198} Chain breaks: 1 Chain: "D" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1770 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 200} Chain breaks: 1 Chain: "E" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1770 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 200} Chain breaks: 1 Chain: "B" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1770 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 200} Chain breaks: 1 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'SPH': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'SPH': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'SPH': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'SPH': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'SPH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.35, per 1000 atoms: 0.59 Number of scatterers: 10754 At special positions: 0 Unit cell: (143.77, 142.463, 99.332, 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 69 16.00 O 1969 8.00 N 1800 7.00 C 6916 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.05 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " 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: 3.98 Conformation dependent library (CDL) restraints added in 2.0 seconds 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2502 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 17 sheets defined 7.9% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.541A pdb=" N PHE A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 80 through 84' Processing helix chain 'A' and resid 117 through 123 removed outlier: 3.649A pdb=" N LYS A 122 " --> pdb=" O GLN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 226 through 228 No H-bonds generated for 'chain 'A' and resid 226 through 228' Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.540A pdb=" N PHE C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 80 through 84' Processing helix chain 'C' and resid 117 through 123 removed outlier: 3.649A pdb=" N LYS C 122 " --> pdb=" O GLN C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 216 through 218 No H-bonds generated for 'chain 'C' and resid 216 through 218' Processing helix chain 'C' and resid 226 through 228 No H-bonds generated for 'chain 'C' and resid 226 through 228' Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.541A pdb=" N PHE D 84 " --> pdb=" O ILE D 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 80 through 84' Processing helix chain 'D' and resid 117 through 123 removed outlier: 3.649A pdb=" N LYS D 122 " --> pdb=" O GLN D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 172 No H-bonds generated for 'chain 'D' and resid 170 through 172' Processing helix chain 'D' and resid 216 through 218 No H-bonds generated for 'chain 'D' and resid 216 through 218' Processing helix chain 'D' and resid 226 through 228 No H-bonds generated for 'chain 'D' and resid 226 through 228' Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.542A pdb=" N PHE E 84 " --> pdb=" O ILE E 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 80 through 84' Processing helix chain 'E' and resid 117 through 123 removed outlier: 3.649A pdb=" N LYS E 122 " --> pdb=" O GLN E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 172 No H-bonds generated for 'chain 'E' and resid 170 through 172' Processing helix chain 'E' and resid 216 through 218 No H-bonds generated for 'chain 'E' and resid 216 through 218' Processing helix chain 'E' and resid 226 through 228 No H-bonds generated for 'chain 'E' and resid 226 through 228' Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.542A pdb=" N PHE B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 80 through 84' Processing helix chain 'B' and resid 117 through 123 removed outlier: 3.648A pdb=" N LYS B 122 " --> pdb=" O GLN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 216 through 218 No H-bonds generated for 'chain 'B' and resid 216 through 218' Processing helix chain 'B' and resid 226 through 228 No H-bonds generated for 'chain 'B' and resid 226 through 228' Processing sheet with id= A, first strand: chain 'H' and resid 36 through 40 removed outlier: 3.733A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS H 38 " --> pdb=" O GLU H 46 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 92 through 94 removed outlier: 3.678A pdb=" N ALA H 92 " --> pdb=" O VAL H 116 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 106 through 110 removed outlier: 3.654A pdb=" N VAL A 181 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 128 through 130 Processing sheet with id= E, first strand: chain 'A' and resid 188 through 190 removed outlier: 3.741A pdb=" N ALA A 188 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 91 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N MET A 253 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU A 89 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 106 through 110 removed outlier: 3.655A pdb=" N VAL C 181 " --> pdb=" O LEU C 151 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 128 through 130 Processing sheet with id= H, first strand: chain 'C' and resid 188 through 190 removed outlier: 3.741A pdb=" N ALA C 188 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER C 91 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET C 253 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU C 89 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 106 through 110 removed outlier: 3.654A pdb=" N VAL D 181 " --> pdb=" O LEU D 151 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 128 through 130 Processing sheet with id= K, first strand: chain 'D' and resid 188 through 190 removed outlier: 3.741A pdb=" N ALA D 188 " --> pdb=" O PHE D 137 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER D 91 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET D 253 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU D 89 " --> pdb=" O MET D 253 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 106 through 110 removed outlier: 3.655A pdb=" N VAL E 181 " --> pdb=" O LEU E 151 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 128 through 130 Processing sheet with id= N, first strand: chain 'E' and resid 188 through 190 removed outlier: 3.741A pdb=" N ALA E 188 " --> pdb=" O PHE E 137 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER E 91 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET E 253 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU E 89 " --> pdb=" O MET E 253 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 106 through 110 removed outlier: 3.655A pdb=" N VAL B 181 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 128 through 130 Processing sheet with id= Q, first strand: chain 'B' and resid 188 through 190 removed outlier: 3.741A pdb=" N ALA B 188 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER B 91 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET B 253 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU B 89 " --> pdb=" O MET B 253 " (cutoff:3.500A) 192 hydrogen bonds defined for protein. 495 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: 2.43 Time building geometry restraints manager: 4.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 1697 1.31 - 1.45: 3295 1.45 - 1.59: 5961 1.59 - 1.72: 0 1.72 - 1.86: 119 Bond restraints: 11072 Sorted by residual: bond pdb=" N SER L 58 " pdb=" CA SER L 58 " ideal model delta sigma weight residual 1.457 1.356 0.101 1.29e-02 6.01e+03 6.16e+01 bond pdb=" C ASN H 52 " pdb=" N PRO H 53 " ideal model delta sigma weight residual 1.333 1.376 -0.043 7.80e-03 1.64e+04 3.04e+01 bond pdb=" C PRO A 148 " pdb=" O PRO A 148 " ideal model delta sigma weight residual 1.233 1.174 0.059 1.13e-02 7.83e+03 2.71e+01 bond pdb=" N GLU L 61 " pdb=" CA GLU L 61 " ideal model delta sigma weight residual 1.458 1.395 0.063 1.24e-02 6.50e+03 2.55e+01 bond pdb=" CA SER B 74 " pdb=" C SER B 74 " ideal model delta sigma weight residual 1.524 1.460 0.064 1.33e-02 5.65e+03 2.28e+01 ... (remaining 11067 not shown) Histogram of bond angle deviations from ideal: 80.97 - 93.37: 1 93.37 - 105.76: 409 105.76 - 118.16: 7903 118.16 - 130.55: 6668 130.55 - 142.95: 60 Bond angle restraints: 15041 Sorted by residual: angle pdb=" N THR L 59 " pdb=" CA THR L 59 " pdb=" C THR L 59 " ideal model delta sigma weight residual 107.67 80.97 26.70 2.09e+00 2.29e-01 1.63e+02 angle pdb=" N ILE L 54 " pdb=" CA ILE L 54 " pdb=" C ILE L 54 " ideal model delta sigma weight residual 110.72 121.14 -10.42 1.01e+00 9.80e-01 1.07e+02 angle pdb=" C VAL L 64 " pdb=" N PRO L 65 " pdb=" CA PRO L 65 " ideal model delta sigma weight residual 119.84 107.91 11.93 1.25e+00 6.40e-01 9.11e+01 angle pdb=" N THR H 69 " pdb=" CA THR H 69 " pdb=" C THR H 69 " ideal model delta sigma weight residual 110.42 96.54 13.88 1.46e+00 4.69e-01 9.04e+01 angle pdb=" N ASN H 61 " pdb=" CA ASN H 61 " pdb=" C ASN H 61 " ideal model delta sigma weight residual 112.86 102.76 10.10 1.22e+00 6.72e-01 6.85e+01 ... (remaining 15036 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5830 17.98 - 35.95: 595 35.95 - 53.93: 128 53.93 - 71.91: 25 71.91 - 89.88: 13 Dihedral angle restraints: 6591 sinusoidal: 2694 harmonic: 3897 Sorted by residual: dihedral pdb=" CA ASP H 50 " pdb=" C ASP H 50 " pdb=" N ILE H 51 " pdb=" CA ILE H 51 " ideal model delta harmonic sigma weight residual -180.00 -119.18 -60.82 0 5.00e+00 4.00e-02 1.48e+02 dihedral pdb=" CA TYR L 98 " pdb=" C TYR L 98 " pdb=" N ASN L 99 " pdb=" CA ASN L 99 " ideal model delta harmonic sigma weight residual -180.00 -124.96 -55.04 0 5.00e+00 4.00e-02 1.21e+02 dihedral pdb=" CA LEU L 79 " pdb=" C LEU L 79 " pdb=" N THR L 80 " pdb=" CA THR L 80 " ideal model delta harmonic sigma weight residual -180.00 -142.99 -37.01 0 5.00e+00 4.00e-02 5.48e+01 ... (remaining 6588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 1502 0.132 - 0.263: 61 0.263 - 0.395: 16 0.395 - 0.527: 2 0.527 - 0.658: 1 Chirality restraints: 1582 Sorted by residual: chirality pdb=" CA PHE H 64 " pdb=" N PHE H 64 " pdb=" C PHE H 64 " pdb=" CB PHE H 64 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA PHE H 59 " pdb=" N PHE H 59 " pdb=" C PHE H 59 " pdb=" CB PHE H 59 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.45e+00 chirality pdb=" CA GLN H 62 " pdb=" N GLN H 62 " pdb=" C GLN H 62 " pdb=" CB GLN H 62 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.61e+00 ... (remaining 1579 not shown) Planarity restraints: 1927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA L 57 " -0.022 2.00e-02 2.50e+03 5.11e-02 2.61e+01 pdb=" C ALA L 57 " 0.088 2.00e-02 2.50e+03 pdb=" O ALA L 57 " -0.036 2.00e-02 2.50e+03 pdb=" N SER L 58 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR L 98 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C TYR L 98 " 0.059 2.00e-02 2.50e+03 pdb=" O TYR L 98 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN L 99 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU L 52 " 0.015 2.00e-02 2.50e+03 3.16e-02 9.97e+00 pdb=" C LEU L 52 " -0.055 2.00e-02 2.50e+03 pdb=" O LEU L 52 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU L 53 " 0.018 2.00e-02 2.50e+03 ... (remaining 1924 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 29 2.43 - 3.05: 6041 3.05 - 3.66: 15069 3.66 - 4.28: 21737 4.28 - 4.90: 36666 Nonbonded interactions: 79542 Sorted by model distance: nonbonded pdb=" O LYS H 67 " pdb=" O GLN H 82 " model vdw 1.810 3.040 nonbonded pdb=" CG PRO L 50 " pdb=" OG1 THR L 59 " model vdw 2.077 3.440 nonbonded pdb=" O ALA H 68 " pdb=" C THR H 69 " model vdw 2.175 3.270 nonbonded pdb=" O ALA L 57 " pdb=" O SER L 58 " model vdw 2.240 3.040 nonbonded pdb=" O SER L 32 " pdb=" OH TYR L 97 " model vdw 2.247 2.440 ... (remaining 79537 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' and (resid 71 through 295 or resid 301)) selection = chain 'C' selection = (chain 'D' and (resid 71 through 295 or resid 301)) selection = (chain 'E' and (resid 71 through 295 or resid 301)) } 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: 0.090 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: 1.360 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 31.240 Find NCS groups from input model: 0.830 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 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 : 0.007 0.101 11072 Z= 0.479 Angle : 1.130 26.699 15041 Z= 0.645 Chirality : 0.072 0.658 1582 Planarity : 0.009 0.079 1927 Dihedral : 15.340 89.881 4083 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.74 % Favored : 92.72 % Rotamer: Outliers : 2.05 % Allowed : 9.12 % Favored : 88.83 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.42 (0.19), residues: 1305 helix: -4.97 (0.10), residues: 100 sheet: -1.75 (0.27), residues: 326 loop : -3.40 (0.16), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 102 HIS 0.004 0.001 HIS B 245 PHE 0.032 0.002 PHE H 107 TYR 0.040 0.002 TYR L 55 ARG 0.003 0.001 ARG C 254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 369 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 39 LEU cc_start: 0.7238 (tp) cc_final: 0.6551 (tp) REVERT: L 44 GLN cc_start: 0.6787 (mp10) cc_final: 0.6564 (mp10) REVERT: L 98 TYR cc_start: 0.6329 (t80) cc_final: 0.5983 (t80) REVERT: H 33 TYR cc_start: 0.7319 (m-10) cc_final: 0.7109 (m-10) REVERT: H 57 ASP cc_start: 0.8592 (p0) cc_final: 0.8204 (p0) REVERT: A 173 THR cc_start: 0.9302 (p) cc_final: 0.9012 (p) REVERT: A 229 MET cc_start: 0.8722 (mtt) cc_final: 0.8502 (mtm) REVERT: A 235 ILE cc_start: 0.9388 (pt) cc_final: 0.9171 (pt) REVERT: A 291 ARG cc_start: 0.8761 (ptt180) cc_final: 0.8548 (ptt-90) REVERT: C 80 ILE cc_start: 0.6303 (mp) cc_final: 0.6069 (mp) REVERT: C 129 MET cc_start: 0.8564 (ttm) cc_final: 0.8246 (mtm) REVERT: C 222 TYR cc_start: 0.8813 (t80) cc_final: 0.8499 (t80) REVERT: C 279 TYR cc_start: 0.8444 (p90) cc_final: 0.8206 (p90) REVERT: C 280 LYS cc_start: 0.8540 (tttt) cc_final: 0.7629 (tptt) REVERT: D 124 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7913 (mt-10) REVERT: D 216 GLN cc_start: 0.8329 (tp-100) cc_final: 0.7738 (tp40) REVERT: D 279 TYR cc_start: 0.8755 (p90) cc_final: 0.8251 (p90) REVERT: D 291 ARG cc_start: 0.8412 (ptt180) cc_final: 0.7325 (ptt90) REVERT: D 293 LYS cc_start: 0.8370 (mttp) cc_final: 0.7904 (ttmm) REVERT: E 229 MET cc_start: 0.8980 (mtt) cc_final: 0.8778 (mtt) REVERT: B 229 MET cc_start: 0.8200 (mtt) cc_final: 0.7843 (mpp) REVERT: B 274 LYS cc_start: 0.9064 (mttt) cc_final: 0.8674 (mtmm) REVERT: B 280 LYS cc_start: 0.8293 (tttt) cc_final: 0.7791 (tptt) REVERT: B 290 SER cc_start: 0.7894 (t) cc_final: 0.7492 (t) outliers start: 24 outliers final: 7 residues processed: 388 average time/residue: 0.2060 time to fit residues: 114.7264 Evaluate side-chains 298 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 291 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain H residue 61 ASN Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain B residue 141 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 20.0000 chunk 99 optimal weight: 8.9990 chunk 55 optimal weight: 0.0980 chunk 33 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 99 ASN H 60 ASN A 73 HIS A 82 ASN A 269 GLN C 71 ASN C 82 ASN C 216 GLN C 224 GLN C 245 HIS ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 GLN D 224 GLN ** D 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN E 216 GLN E 224 GLN B 71 ASN B 176 ASN B 245 HIS B 257 HIS ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 11072 Z= 0.301 Angle : 0.736 11.500 15041 Z= 0.378 Chirality : 0.048 0.264 1582 Planarity : 0.006 0.065 1927 Dihedral : 8.351 57.496 1555 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.20 % Favored : 91.34 % Rotamer: Outliers : 4.43 % Allowed : 17.31 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.49 % 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: -3.56 (0.20), residues: 1305 helix: -4.19 (0.25), residues: 100 sheet: -1.00 (0.26), residues: 357 loop : -2.94 (0.18), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 261 HIS 0.002 0.001 HIS A 72 PHE 0.013 0.001 PHE H 64 TYR 0.035 0.002 TYR L 100 ARG 0.006 0.000 ARG C 264 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 318 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 32 TYR cc_start: 0.6051 (p90) cc_final: 0.5723 (p90) REVERT: H 33 TYR cc_start: 0.7678 (m-10) cc_final: 0.7260 (m-10) REVERT: H 34 MET cc_start: 0.6835 (OUTLIER) cc_final: 0.6403 (ttp) REVERT: H 57 ASP cc_start: 0.8519 (p0) cc_final: 0.7992 (p0) REVERT: H 59 PHE cc_start: 0.7278 (OUTLIER) cc_final: 0.6620 (m-80) REVERT: A 134 GLU cc_start: 0.7880 (tt0) cc_final: 0.7638 (tt0) REVERT: A 167 ASP cc_start: 0.8058 (p0) cc_final: 0.7766 (p0) REVERT: A 280 LYS cc_start: 0.6334 (tptt) cc_final: 0.5625 (tptt) REVERT: C 122 LYS cc_start: 0.8788 (mtpt) cc_final: 0.7851 (mmtt) REVERT: C 124 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7891 (mt-10) REVERT: C 191 SER cc_start: 0.8539 (m) cc_final: 0.8243 (t) REVERT: C 206 ASP cc_start: 0.8273 (t0) cc_final: 0.7797 (t70) REVERT: C 222 TYR cc_start: 0.8910 (t80) cc_final: 0.8616 (t80) REVERT: C 242 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8258 (tttt) REVERT: C 280 LYS cc_start: 0.8523 (tttt) cc_final: 0.7673 (tptt) REVERT: D 124 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8054 (mt-10) REVERT: D 167 ASP cc_start: 0.8253 (p0) cc_final: 0.8028 (p0) REVERT: D 183 MET cc_start: 0.8446 (mtp) cc_final: 0.8139 (mtm) REVERT: D 195 MET cc_start: 0.8703 (ptm) cc_final: 0.8462 (ptp) REVERT: D 279 TYR cc_start: 0.8877 (p90) cc_final: 0.8184 (p90) REVERT: D 293 LYS cc_start: 0.8569 (mttp) cc_final: 0.8125 (tptp) REVERT: E 229 MET cc_start: 0.9029 (mtt) cc_final: 0.8750 (mpp) REVERT: B 229 MET cc_start: 0.8344 (mtt) cc_final: 0.7899 (mpp) REVERT: B 274 LYS cc_start: 0.9246 (mttt) cc_final: 0.9035 (mtmt) REVERT: B 280 LYS cc_start: 0.8286 (tttt) cc_final: 0.7841 (tptt) outliers start: 52 outliers final: 33 residues processed: 346 average time/residue: 0.2074 time to fit residues: 103.5045 Evaluate side-chains 334 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 298 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 275 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 20.0000 chunk 36 optimal weight: 0.2980 chunk 99 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 32 optimal weight: 50.0000 chunk 119 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 118 optimal weight: 0.3980 chunk 40 optimal weight: 6.9990 chunk 95 optimal weight: 20.0000 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 99 ASN H 61 ASN H 62 GLN A 73 HIS A 278 ASN C 82 ASN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11072 Z= 0.202 Angle : 0.660 10.641 15041 Z= 0.337 Chirality : 0.046 0.234 1582 Planarity : 0.005 0.058 1927 Dihedral : 7.431 52.821 1541 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.97 % Favored : 92.72 % Rotamer: Outliers : 4.18 % Allowed : 20.12 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.49 % 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: -3.03 (0.21), residues: 1305 helix: -3.54 (0.35), residues: 100 sheet: -0.62 (0.27), residues: 360 loop : -2.62 (0.19), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 102 HIS 0.002 0.000 HIS B 73 PHE 0.014 0.001 PHE A 233 TYR 0.031 0.001 TYR H 80 ARG 0.008 0.000 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 320 time to evaluate : 1.317 Fit side-chains revert: symmetry clash REVERT: L 29 LEU cc_start: 0.5265 (OUTLIER) cc_final: 0.4689 (pp) REVERT: L 76 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7131 (m-30) REVERT: H 32 TYR cc_start: 0.5911 (p90) cc_final: 0.5670 (p90) REVERT: H 33 TYR cc_start: 0.7579 (m-10) cc_final: 0.7279 (m-10) REVERT: H 34 MET cc_start: 0.6923 (OUTLIER) cc_final: 0.6567 (ttp) REVERT: H 38 LYS cc_start: 0.7090 (ttpp) cc_final: 0.6831 (ttpp) REVERT: H 39 GLN cc_start: 0.7787 (pp30) cc_final: 0.6928 (pp30) REVERT: H 46 GLU cc_start: 0.6886 (pm20) cc_final: 0.6670 (pm20) REVERT: H 57 ASP cc_start: 0.8420 (p0) cc_final: 0.7918 (p0) REVERT: H 83 LEU cc_start: 0.7070 (pt) cc_final: 0.6791 (pt) REVERT: A 280 LYS cc_start: 0.6365 (tptt) cc_final: 0.6005 (tptt) REVERT: C 124 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7936 (mt-10) REVERT: C 129 MET cc_start: 0.8432 (mtp) cc_final: 0.8107 (mtm) REVERT: C 206 ASP cc_start: 0.8445 (t0) cc_final: 0.7987 (t70) REVERT: C 216 GLN cc_start: 0.8762 (tp-100) cc_final: 0.8288 (tp40) REVERT: C 222 TYR cc_start: 0.8877 (t80) cc_final: 0.8561 (t80) REVERT: C 271 TYR cc_start: 0.8856 (m-80) cc_final: 0.8652 (m-80) REVERT: C 280 LYS cc_start: 0.8359 (tttt) cc_final: 0.7488 (tptt) REVERT: D 183 MET cc_start: 0.8599 (mtp) cc_final: 0.8387 (mtm) REVERT: D 279 TYR cc_start: 0.8723 (p90) cc_final: 0.8194 (p90) REVERT: D 293 LYS cc_start: 0.8487 (mttp) cc_final: 0.7980 (tptp) REVERT: E 134 GLU cc_start: 0.8371 (tt0) cc_final: 0.8002 (tt0) REVERT: E 222 TYR cc_start: 0.8778 (t80) cc_final: 0.8477 (t80) REVERT: E 229 MET cc_start: 0.8993 (mtt) cc_final: 0.8651 (mpp) REVERT: B 229 MET cc_start: 0.8314 (mtt) cc_final: 0.7879 (mpp) REVERT: B 280 LYS cc_start: 0.8252 (tttt) cc_final: 0.7719 (tptt) outliers start: 49 outliers final: 35 residues processed: 343 average time/residue: 0.2052 time to fit residues: 102.5323 Evaluate side-chains 346 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 308 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 235 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 13 optimal weight: 40.0000 chunk 56 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 126 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 113 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11072 Z= 0.287 Angle : 0.682 10.792 15041 Z= 0.348 Chirality : 0.046 0.236 1582 Planarity : 0.005 0.056 1927 Dihedral : 7.371 50.464 1541 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.28 % Favored : 91.57 % Rotamer: Outliers : 6.31 % Allowed : 18.41 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.33 % 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: -2.71 (0.22), residues: 1305 helix: -3.01 (0.43), residues: 100 sheet: -0.41 (0.27), residues: 345 loop : -2.40 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 56 HIS 0.003 0.001 HIS E 257 PHE 0.013 0.001 PHE L 104 TYR 0.031 0.002 TYR L 100 ARG 0.006 0.000 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 324 time to evaluate : 1.306 Fit side-chains revert: symmetry clash REVERT: L 29 LEU cc_start: 0.5376 (OUTLIER) cc_final: 0.4768 (pp) REVERT: L 76 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7078 (m-30) REVERT: H 32 TYR cc_start: 0.6116 (p90) cc_final: 0.5828 (p90) REVERT: H 34 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6791 (ttp) REVERT: H 38 LYS cc_start: 0.7066 (ttpp) cc_final: 0.6662 (ttpp) REVERT: H 39 GLN cc_start: 0.7893 (pp30) cc_final: 0.7024 (pp30) REVERT: H 46 GLU cc_start: 0.6896 (pm20) cc_final: 0.6617 (pm20) REVERT: H 57 ASP cc_start: 0.8422 (p0) cc_final: 0.7800 (p0) REVERT: H 83 LEU cc_start: 0.7088 (pt) cc_final: 0.6813 (pt) REVERT: A 134 GLU cc_start: 0.8027 (tt0) cc_final: 0.7573 (tt0) REVERT: A 154 MET cc_start: 0.8800 (ttt) cc_final: 0.8507 (ttt) REVERT: A 224 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8466 (mm-40) REVERT: A 280 LYS cc_start: 0.6530 (tptt) cc_final: 0.5977 (tptt) REVERT: A 290 SER cc_start: 0.7957 (t) cc_final: 0.7592 (m) REVERT: C 122 LYS cc_start: 0.8858 (mtpt) cc_final: 0.7860 (mmtt) REVERT: C 206 ASP cc_start: 0.8516 (t0) cc_final: 0.8142 (t70) REVERT: C 216 GLN cc_start: 0.8633 (tp-100) cc_final: 0.8360 (tp-100) REVERT: C 222 TYR cc_start: 0.8970 (t80) cc_final: 0.8426 (t80) REVERT: C 280 LYS cc_start: 0.8432 (tttt) cc_final: 0.7603 (tptt) REVERT: C 283 ASP cc_start: 0.7939 (t0) cc_final: 0.7603 (t0) REVERT: D 108 ASN cc_start: 0.8092 (t0) cc_final: 0.7786 (t0) REVERT: D 167 ASP cc_start: 0.8183 (p0) cc_final: 0.7974 (p0) REVERT: D 183 MET cc_start: 0.8562 (mtp) cc_final: 0.8282 (mtm) REVERT: D 279 TYR cc_start: 0.8759 (p90) cc_final: 0.8141 (p90) REVERT: D 293 LYS cc_start: 0.8400 (mttp) cc_final: 0.7961 (tptp) REVERT: E 222 TYR cc_start: 0.8744 (t80) cc_final: 0.8543 (t80) REVERT: E 229 MET cc_start: 0.9062 (mtt) cc_final: 0.8839 (mtt) REVERT: B 110 ASP cc_start: 0.8799 (t0) cc_final: 0.8563 (t0) REVERT: B 229 MET cc_start: 0.8416 (mtt) cc_final: 0.7872 (mpp) REVERT: B 274 LYS cc_start: 0.9312 (mtmt) cc_final: 0.9054 (ttmt) REVERT: B 280 LYS cc_start: 0.8304 (tttt) cc_final: 0.7822 (tptt) outliers start: 74 outliers final: 57 residues processed: 359 average time/residue: 0.1962 time to fit residues: 102.4001 Evaluate side-chains 372 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 312 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 275 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 87 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 64 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 GLN E 76 GLN E 82 ASN ** E 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11072 Z= 0.256 Angle : 0.679 10.401 15041 Z= 0.340 Chirality : 0.046 0.231 1582 Planarity : 0.005 0.059 1927 Dihedral : 7.182 50.170 1541 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.89 % Favored : 91.95 % Rotamer: Outliers : 6.05 % Allowed : 19.69 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.16 % 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: -2.47 (0.22), residues: 1305 helix: -2.65 (0.48), residues: 100 sheet: -0.30 (0.28), residues: 340 loop : -2.22 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 56 HIS 0.003 0.001 HIS E 257 PHE 0.011 0.001 PHE L 104 TYR 0.028 0.001 TYR L 100 ARG 0.006 0.000 ARG C 264 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 328 time to evaluate : 1.303 Fit side-chains revert: symmetry clash REVERT: L 29 LEU cc_start: 0.5400 (OUTLIER) cc_final: 0.4819 (pp) REVERT: L 76 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.7044 (m-30) REVERT: H 38 LYS cc_start: 0.6837 (ttpp) cc_final: 0.6552 (ttpp) REVERT: H 39 GLN cc_start: 0.7883 (pp30) cc_final: 0.6925 (pp30) REVERT: H 46 GLU cc_start: 0.6840 (pm20) cc_final: 0.6610 (pm20) REVERT: H 57 ASP cc_start: 0.8376 (p0) cc_final: 0.7704 (p0) REVERT: H 83 LEU cc_start: 0.6997 (pt) cc_final: 0.6793 (pt) REVERT: A 224 GLN cc_start: 0.8943 (mm110) cc_final: 0.8648 (mm-40) REVERT: A 280 LYS cc_start: 0.6522 (tptt) cc_final: 0.5943 (tptt) REVERT: C 110 ASP cc_start: 0.9109 (t0) cc_final: 0.8865 (t0) REVERT: C 206 ASP cc_start: 0.8500 (t0) cc_final: 0.8008 (t70) REVERT: C 216 GLN cc_start: 0.8609 (tp-100) cc_final: 0.8260 (tp-100) REVERT: C 222 TYR cc_start: 0.8940 (t80) cc_final: 0.8182 (t80) REVERT: C 224 GLN cc_start: 0.8962 (mm-40) cc_final: 0.8293 (mm-40) REVERT: C 280 LYS cc_start: 0.8534 (tttt) cc_final: 0.7612 (tptt) REVERT: C 283 ASP cc_start: 0.8153 (t0) cc_final: 0.7819 (t0) REVERT: D 108 ASN cc_start: 0.8255 (t0) cc_final: 0.7966 (t0) REVERT: D 124 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7965 (mt-10) REVERT: D 167 ASP cc_start: 0.8292 (p0) cc_final: 0.8035 (p0) REVERT: D 274 LYS cc_start: 0.9142 (mttm) cc_final: 0.8485 (mtmm) REVERT: D 279 TYR cc_start: 0.8723 (p90) cc_final: 0.8150 (p90) REVERT: D 293 LYS cc_start: 0.8400 (mttp) cc_final: 0.7971 (tptp) REVERT: E 222 TYR cc_start: 0.8738 (t80) cc_final: 0.8535 (t80) REVERT: E 229 MET cc_start: 0.9060 (mtt) cc_final: 0.8855 (mtt) REVERT: B 110 ASP cc_start: 0.8828 (t0) cc_final: 0.8586 (t0) REVERT: B 229 MET cc_start: 0.8316 (mtt) cc_final: 0.7791 (mpp) REVERT: B 274 LYS cc_start: 0.9303 (mtmt) cc_final: 0.9059 (ttmt) REVERT: B 280 LYS cc_start: 0.8292 (tttt) cc_final: 0.7794 (tptt) outliers start: 71 outliers final: 54 residues processed: 362 average time/residue: 0.1949 time to fit residues: 102.6608 Evaluate side-chains 374 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 318 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 235 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 41 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN E 82 ASN ** E 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11072 Z= 0.314 Angle : 0.703 10.611 15041 Z= 0.351 Chirality : 0.047 0.288 1582 Planarity : 0.005 0.058 1927 Dihedral : 7.256 48.002 1541 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.50 % Favored : 90.34 % Rotamer: Outliers : 6.48 % Allowed : 19.61 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.25 % 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: -2.32 (0.22), residues: 1305 helix: -2.48 (0.50), residues: 100 sheet: -0.16 (0.28), residues: 334 loop : -2.12 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 56 HIS 0.004 0.001 HIS E 257 PHE 0.009 0.001 PHE B 233 TYR 0.029 0.002 TYR L 100 ARG 0.005 0.001 ARG C 264 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 321 time to evaluate : 1.312 Fit side-chains REVERT: L 29 LEU cc_start: 0.5559 (OUTLIER) cc_final: 0.4961 (pp) REVERT: L 76 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.6992 (m-30) REVERT: H 57 ASP cc_start: 0.8377 (p0) cc_final: 0.7803 (p0) REVERT: A 224 GLN cc_start: 0.8931 (mm110) cc_final: 0.8617 (mm-40) REVERT: A 280 LYS cc_start: 0.6630 (tptt) cc_final: 0.5952 (tptt) REVERT: C 122 LYS cc_start: 0.8869 (mtpt) cc_final: 0.7830 (mmtt) REVERT: C 206 ASP cc_start: 0.8509 (t0) cc_final: 0.8006 (t70) REVERT: C 216 GLN cc_start: 0.8630 (tp-100) cc_final: 0.8270 (tp-100) REVERT: C 222 TYR cc_start: 0.8973 (t80) cc_final: 0.8406 (t80) REVERT: C 224 GLN cc_start: 0.8969 (mm-40) cc_final: 0.8571 (mm110) REVERT: C 280 LYS cc_start: 0.8594 (tttt) cc_final: 0.7649 (tptt) REVERT: C 283 ASP cc_start: 0.8274 (t0) cc_final: 0.8020 (t0) REVERT: D 108 ASN cc_start: 0.8341 (t0) cc_final: 0.8039 (t0) REVERT: D 167 ASP cc_start: 0.8324 (p0) cc_final: 0.8088 (p0) REVERT: D 279 TYR cc_start: 0.8816 (p90) cc_final: 0.8246 (p90) REVERT: D 293 LYS cc_start: 0.8412 (mttp) cc_final: 0.7971 (tptp) REVERT: E 183 MET cc_start: 0.8847 (ttm) cc_final: 0.7903 (mtp) REVERT: E 229 MET cc_start: 0.9102 (mtt) cc_final: 0.8834 (mtt) REVERT: B 110 ASP cc_start: 0.8912 (t0) cc_final: 0.8644 (t0) REVERT: B 141 LYS cc_start: 0.9051 (mtpt) cc_final: 0.8844 (mtpt) REVERT: B 229 MET cc_start: 0.8370 (mtt) cc_final: 0.7770 (mpp) REVERT: B 274 LYS cc_start: 0.9315 (mtmt) cc_final: 0.9080 (ttmt) REVERT: B 280 LYS cc_start: 0.8335 (tttt) cc_final: 0.7812 (tptt) outliers start: 76 outliers final: 63 residues processed: 354 average time/residue: 0.2032 time to fit residues: 103.7451 Evaluate side-chains 380 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 315 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 297 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 58 optimal weight: 0.0040 overall best weight: 4.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN E 76 GLN E 82 ASN E 218 ASN ** E 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11072 Z= 0.257 Angle : 0.685 12.081 15041 Z= 0.339 Chirality : 0.046 0.254 1582 Planarity : 0.005 0.055 1927 Dihedral : 7.108 46.318 1541 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.51 % Favored : 91.34 % Rotamer: Outliers : 5.71 % Allowed : 20.63 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.16 % 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: -2.22 (0.23), residues: 1305 helix: -2.42 (0.50), residues: 100 sheet: -0.14 (0.28), residues: 337 loop : -2.04 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 56 HIS 0.003 0.001 HIS E 257 PHE 0.011 0.001 PHE B 233 TYR 0.027 0.001 TYR L 100 ARG 0.007 0.000 ARG C 264 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 321 time to evaluate : 1.354 Fit side-chains REVERT: L 29 LEU cc_start: 0.5529 (OUTLIER) cc_final: 0.4933 (pp) REVERT: L 76 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7010 (m-30) REVERT: H 34 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.7112 (ttp) REVERT: H 57 ASP cc_start: 0.8284 (p0) cc_final: 0.7734 (p0) REVERT: A 280 LYS cc_start: 0.6644 (tptt) cc_final: 0.6119 (tptt) REVERT: C 206 ASP cc_start: 0.8503 (t0) cc_final: 0.8019 (t70) REVERT: C 216 GLN cc_start: 0.8633 (tp-100) cc_final: 0.8251 (tp-100) REVERT: C 222 TYR cc_start: 0.9010 (t80) cc_final: 0.8435 (t80) REVERT: C 224 GLN cc_start: 0.8983 (mm-40) cc_final: 0.8399 (mm-40) REVERT: C 280 LYS cc_start: 0.8624 (tttt) cc_final: 0.7713 (tptt) REVERT: D 108 ASN cc_start: 0.8318 (t0) cc_final: 0.8032 (t0) REVERT: D 167 ASP cc_start: 0.8306 (p0) cc_final: 0.8081 (p0) REVERT: D 279 TYR cc_start: 0.8763 (p90) cc_final: 0.8227 (p90) REVERT: D 293 LYS cc_start: 0.8384 (mttp) cc_final: 0.7953 (tptp) REVERT: E 183 MET cc_start: 0.8743 (ttm) cc_final: 0.7843 (mtp) REVERT: E 229 MET cc_start: 0.9096 (mtt) cc_final: 0.8777 (mtt) REVERT: B 229 MET cc_start: 0.8352 (mtt) cc_final: 0.7756 (mpp) REVERT: B 274 LYS cc_start: 0.9328 (mtmt) cc_final: 0.9063 (ttmt) REVERT: B 280 LYS cc_start: 0.8289 (tttt) cc_final: 0.7766 (tptt) outliers start: 67 outliers final: 55 residues processed: 353 average time/residue: 0.1981 time to fit residues: 101.7132 Evaluate side-chains 371 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 313 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 275 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN ** E 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11072 Z= 0.280 Angle : 0.692 10.304 15041 Z= 0.343 Chirality : 0.046 0.213 1582 Planarity : 0.005 0.054 1927 Dihedral : 7.089 47.569 1541 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.12 % Favored : 90.73 % Rotamer: Outliers : 5.88 % Allowed : 20.89 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.16 % 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: -2.15 (0.23), residues: 1305 helix: -2.40 (0.50), residues: 100 sheet: -0.18 (0.29), residues: 325 loop : -1.93 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 56 HIS 0.003 0.001 HIS E 257 PHE 0.010 0.001 PHE B 233 TYR 0.028 0.001 TYR L 100 ARG 0.005 0.000 ARG C 264 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 317 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 29 LEU cc_start: 0.5645 (OUTLIER) cc_final: 0.5049 (pp) REVERT: L 101 PRO cc_start: 0.5031 (Cg_endo) cc_final: 0.4825 (Cg_exo) REVERT: H 34 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.7108 (ttp) REVERT: H 57 ASP cc_start: 0.8269 (p0) cc_final: 0.7765 (p0) REVERT: A 280 LYS cc_start: 0.6514 (tptt) cc_final: 0.5901 (tptt) REVERT: C 206 ASP cc_start: 0.8505 (t0) cc_final: 0.8027 (t70) REVERT: C 216 GLN cc_start: 0.8634 (tp-100) cc_final: 0.8240 (tp-100) REVERT: C 222 TYR cc_start: 0.9026 (t80) cc_final: 0.8717 (t80) REVERT: C 280 LYS cc_start: 0.8680 (tttt) cc_final: 0.7804 (tptt) REVERT: D 108 ASN cc_start: 0.8329 (t0) cc_final: 0.8041 (t0) REVERT: D 167 ASP cc_start: 0.8341 (p0) cc_final: 0.8137 (p0) REVERT: D 279 TYR cc_start: 0.8713 (p90) cc_final: 0.8122 (p90) REVERT: D 293 LYS cc_start: 0.8367 (mtpp) cc_final: 0.7961 (tptp) REVERT: E 183 MET cc_start: 0.8677 (ttm) cc_final: 0.7777 (mtp) REVERT: E 229 MET cc_start: 0.9081 (mtt) cc_final: 0.8777 (mtt) REVERT: B 141 LYS cc_start: 0.8975 (mtpt) cc_final: 0.8766 (mtpt) REVERT: B 274 LYS cc_start: 0.9343 (mtmt) cc_final: 0.9057 (ttmt) REVERT: B 280 LYS cc_start: 0.8325 (tttt) cc_final: 0.7793 (tptt) outliers start: 69 outliers final: 61 residues processed: 351 average time/residue: 0.1994 time to fit residues: 100.6461 Evaluate side-chains 376 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 313 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 275 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 36 optimal weight: 40.0000 chunk 106 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN C 278 ASN D 282 ASN ** E 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11072 Z= 0.312 Angle : 0.718 11.123 15041 Z= 0.355 Chirality : 0.047 0.214 1582 Planarity : 0.005 0.088 1927 Dihedral : 7.180 47.897 1541 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.20 % Favored : 90.65 % Rotamer: Outliers : 5.54 % Allowed : 21.14 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.16 % 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: -2.10 (0.23), residues: 1305 helix: -2.41 (0.50), residues: 100 sheet: -0.17 (0.29), residues: 325 loop : -1.87 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 56 HIS 0.004 0.001 HIS E 257 PHE 0.009 0.001 PHE B 233 TYR 0.030 0.002 TYR L 100 ARG 0.005 0.000 ARG C 264 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 315 time to evaluate : 1.270 Fit side-chains revert: symmetry clash REVERT: L 29 LEU cc_start: 0.5622 (OUTLIER) cc_final: 0.5058 (pp) REVERT: L 101 PRO cc_start: 0.5124 (Cg_endo) cc_final: 0.4835 (Cg_exo) REVERT: A 76 GLN cc_start: 0.8597 (tm-30) cc_final: 0.8222 (tm-30) REVERT: A 280 LYS cc_start: 0.6637 (tptt) cc_final: 0.6018 (tptt) REVERT: C 206 ASP cc_start: 0.8490 (t0) cc_final: 0.8020 (t70) REVERT: C 216 GLN cc_start: 0.8626 (tp-100) cc_final: 0.8232 (tp-100) REVERT: C 222 TYR cc_start: 0.9072 (t80) cc_final: 0.8623 (t80) REVERT: C 224 GLN cc_start: 0.9026 (mm-40) cc_final: 0.8638 (mm-40) REVERT: C 280 LYS cc_start: 0.8676 (tttt) cc_final: 0.7785 (tptt) REVERT: D 108 ASN cc_start: 0.8392 (t0) cc_final: 0.8092 (t0) REVERT: D 167 ASP cc_start: 0.8425 (p0) cc_final: 0.8214 (p0) REVERT: D 222 TYR cc_start: 0.8194 (t80) cc_final: 0.7904 (t80) REVERT: D 279 TYR cc_start: 0.8790 (p90) cc_final: 0.8091 (p90) REVERT: D 293 LYS cc_start: 0.8365 (mtpp) cc_final: 0.7968 (tptp) REVERT: E 183 MET cc_start: 0.8681 (ttm) cc_final: 0.7793 (mtp) REVERT: E 229 MET cc_start: 0.9070 (mtt) cc_final: 0.8785 (mtt) REVERT: B 141 LYS cc_start: 0.8978 (mtpt) cc_final: 0.8730 (mtpt) REVERT: B 274 LYS cc_start: 0.9336 (mtmt) cc_final: 0.9036 (ttmt) REVERT: B 280 LYS cc_start: 0.8324 (tttt) cc_final: 0.7787 (tptt) outliers start: 65 outliers final: 58 residues processed: 346 average time/residue: 0.2062 time to fit residues: 102.3727 Evaluate side-chains 370 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 311 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 275 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 86 optimal weight: 20.0000 chunk 130 optimal weight: 0.0570 chunk 120 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 80 optimal weight: 4.9990 chunk 63 optimal weight: 30.0000 chunk 82 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 overall best weight: 2.8904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN E 218 ASN ** E 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 11072 Z= 0.224 Angle : 0.686 11.438 15041 Z= 0.337 Chirality : 0.046 0.201 1582 Planarity : 0.005 0.085 1927 Dihedral : 6.923 46.203 1541 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.20 % Favored : 90.65 % Rotamer: Outliers : 4.94 % Allowed : 21.65 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.25 % 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: -1.98 (0.23), residues: 1305 helix: -2.39 (0.49), residues: 100 sheet: -0.07 (0.29), residues: 325 loop : -1.78 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP L 56 HIS 0.004 0.001 HIS B 214 PHE 0.013 0.001 PHE B 233 TYR 0.025 0.001 TYR L 100 ARG 0.006 0.000 ARG C 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 326 time to evaluate : 1.326 Fit side-chains revert: symmetry clash REVERT: L 29 LEU cc_start: 0.5596 (OUTLIER) cc_final: 0.5042 (pp) REVERT: L 101 PRO cc_start: 0.4954 (Cg_endo) cc_final: 0.4660 (Cg_exo) REVERT: A 76 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8262 (tm-30) REVERT: A 95 MET cc_start: 0.8400 (tpp) cc_final: 0.7935 (ttt) REVERT: A 280 LYS cc_start: 0.6610 (tptt) cc_final: 0.5971 (tptt) REVERT: C 206 ASP cc_start: 0.8430 (t0) cc_final: 0.7923 (t70) REVERT: C 214 HIS cc_start: 0.8465 (m-70) cc_final: 0.8226 (m-70) REVERT: C 216 GLN cc_start: 0.8593 (tp-100) cc_final: 0.8192 (tp-100) REVERT: C 222 TYR cc_start: 0.9031 (t80) cc_final: 0.8388 (t80) REVERT: C 224 GLN cc_start: 0.9027 (mm-40) cc_final: 0.8410 (mm-40) REVERT: C 280 LYS cc_start: 0.8653 (tttt) cc_final: 0.7775 (tptt) REVERT: D 108 ASN cc_start: 0.8268 (t0) cc_final: 0.8008 (t0) REVERT: D 279 TYR cc_start: 0.8483 (p90) cc_final: 0.7941 (p90) REVERT: D 293 LYS cc_start: 0.8290 (mtpp) cc_final: 0.7924 (tptp) REVERT: E 183 MET cc_start: 0.8627 (ttm) cc_final: 0.7849 (mtp) REVERT: E 229 MET cc_start: 0.9069 (mtt) cc_final: 0.8766 (mtt) REVERT: B 280 LYS cc_start: 0.8306 (tttt) cc_final: 0.7754 (tptt) outliers start: 58 outliers final: 49 residues processed: 355 average time/residue: 0.1852 time to fit residues: 95.5754 Evaluate side-chains 371 residues out of total 1173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 321 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 275 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 chunk 13 optimal weight: 40.0000 chunk 19 optimal weight: 30.0000 chunk 91 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN E 189 GLN E 218 ASN ** E 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 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 = 0.3292 r_free = 0.3292 target = 0.125118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.106051 restraints weight = 17435.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.108624 restraints weight = 7579.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.110182 restraints weight = 4156.984| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 11072 Z= 0.391 Angle : 0.761 11.240 15041 Z= 0.376 Chirality : 0.049 0.210 1582 Planarity : 0.006 0.084 1927 Dihedral : 7.252 49.652 1541 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.27 % Favored : 89.58 % Rotamer: Outliers : 5.20 % Allowed : 22.25 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.16 % 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: -2.08 (0.23), residues: 1305 helix: -2.42 (0.49), residues: 100 sheet: -0.22 (0.29), residues: 331 loop : -1.83 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L 56 HIS 0.005 0.001 HIS B 214 PHE 0.011 0.001 PHE A 135 TYR 0.032 0.002 TYR L 100 ARG 0.005 0.001 ARG A 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2534.04 seconds wall clock time: 47 minutes 31.81 seconds (2851.81 seconds total)