Starting phenix.real_space_refine on Fri Apr 5 13:29:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tdo_41172/04_2024/8tdo_41172.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tdo_41172/04_2024/8tdo_41172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tdo_41172/04_2024/8tdo_41172.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tdo_41172/04_2024/8tdo_41172.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tdo_41172/04_2024/8tdo_41172.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tdo_41172/04_2024/8tdo_41172.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 8 5.16 5 C 1856 2.51 5 N 480 2.21 5 O 548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 89": "OE1" <-> "OE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 99": "OD1" <-> "OD2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 99": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 2892 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 5, 'TRANS': 87} Chain breaks: 1 Chain: "B" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 5, 'TRANS': 87} Chain breaks: 1 Chain: "C" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 5, 'TRANS': 87} Chain breaks: 1 Chain: "E" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 5, 'TRANS': 87} Chain breaks: 1 Time building chain proxies: 2.02, per 1000 atoms: 0.70 Number of scatterers: 2892 At special positions: 0 Unit cell: (78.02, 83.83, 36.52, 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 8 16.00 O 548 8.00 N 480 7.00 C 1856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 503.4 milliseconds 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 712 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 60.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 16 removed outlier: 6.399A pdb=" N LEU A 12 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N LYS B 15 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL A 14 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 19 through 22 removed outlier: 6.253A pdb=" N VAL A 20 " --> pdb=" O ARG B 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 35 removed outlier: 6.419A pdb=" N ALA A 25 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N VAL C 28 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ASN A 27 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL C 30 " --> pdb=" O ASN A 27 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA A 29 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL C 32 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N HIS A 31 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ARG C 34 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N PHE A 33 " --> pdb=" O ARG C 34 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA C 25 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N VAL E 28 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASN C 27 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL E 30 " --> pdb=" O ASN C 27 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA C 29 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL E 32 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N HIS C 31 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ARG E 34 " --> pdb=" O HIS C 31 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE C 33 " --> pdb=" O ARG E 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 80 removed outlier: 6.839A pdb=" N LYS B 70 " --> pdb=" O TYR A 69 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL A 71 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLU B 72 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE A 73 " --> pdb=" O GLU B 72 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TRP A 79 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LYS B 80 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLU A 61 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLU C 62 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLU A 63 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N PHE C 64 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL A 65 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLU C 66 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLY A 67 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE C 68 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TYR A 69 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ASP C 74 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR A 75 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LYS C 76 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER A 77 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N TYR C 78 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR C 60 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N GLU E 63 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLU C 62 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL E 65 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N PHE C 64 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLY E 67 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLU C 66 " --> pdb=" O GLY E 67 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N TYR E 69 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ILE C 68 " --> pdb=" O TYR E 69 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL E 71 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N LYS C 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N ILE E 73 " --> pdb=" O LYS C 70 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLU C 72 " --> pdb=" O ILE E 73 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N THR E 75 " --> pdb=" O GLU C 72 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP C 74 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N SER E 77 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LYS C 76 " --> pdb=" O SER E 77 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N TRP E 79 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N TYR C 78 " --> pdb=" O TRP E 79 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 92 through 99 removed outlier: 6.661A pdb=" N VAL A 93 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N THR C 96 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE A 95 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ASN C 98 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA A 97 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL C 93 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N THR E 96 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE C 95 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ASN E 98 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA C 97 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 103 through 110 removed outlier: 6.632A pdb=" N ARG A 104 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE B 107 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N THR A 106 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ALA B 109 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ALA A 108 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU C 110 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU E 110 " --> pdb=" O ALA C 109 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 118 through 123 removed outlier: 5.728A pdb=" N THR A 118 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL C 121 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA A 120 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N THR C 123 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL A 122 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N THR C 118 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL E 121 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA C 120 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N THR E 123 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL C 122 " --> pdb=" O THR E 123 " (cutoff:3.500A) 68 hydrogen bonds defined for protein. 204 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: 0.67 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 912 1.34 - 1.45: 406 1.45 - 1.57: 1630 1.57 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 2960 Sorted by residual: bond pdb=" CA LYS E 35 " pdb=" C LYS E 35 " ideal model delta sigma weight residual 1.522 1.505 0.017 1.22e-02 6.72e+03 1.97e+00 bond pdb=" CA LYS B 35 " pdb=" C LYS B 35 " ideal model delta sigma weight residual 1.522 1.505 0.017 1.22e-02 6.72e+03 1.83e+00 bond pdb=" C LYS C 35 " pdb=" O LYS C 35 " ideal model delta sigma weight residual 1.235 1.218 0.017 1.28e-02 6.10e+03 1.77e+00 bond pdb=" CA LYS A 35 " pdb=" C LYS A 35 " ideal model delta sigma weight residual 1.522 1.506 0.016 1.22e-02 6.72e+03 1.76e+00 bond pdb=" C LYS A 35 " pdb=" O LYS A 35 " ideal model delta sigma weight residual 1.235 1.218 0.017 1.28e-02 6.10e+03 1.75e+00 ... (remaining 2955 not shown) Histogram of bond angle deviations from ideal: 100.57 - 107.24: 139 107.24 - 113.90: 1683 113.90 - 120.57: 1098 120.57 - 127.23: 1076 127.23 - 133.90: 36 Bond angle restraints: 4032 Sorted by residual: angle pdb=" C TYR E 116 " pdb=" N SER E 117 " pdb=" CA SER E 117 " ideal model delta sigma weight residual 122.53 119.82 2.71 1.61e+00 3.86e-01 2.84e+00 angle pdb=" C ARG A 34 " pdb=" N LYS A 35 " pdb=" CA LYS A 35 " ideal model delta sigma weight residual 122.94 120.44 2.50 1.50e+00 4.44e-01 2.78e+00 angle pdb=" C TYR C 116 " pdb=" N SER C 117 " pdb=" CA SER C 117 " ideal model delta sigma weight residual 122.53 119.86 2.67 1.61e+00 3.86e-01 2.75e+00 angle pdb=" C TYR B 116 " pdb=" N SER B 117 " pdb=" CA SER B 117 " ideal model delta sigma weight residual 122.53 119.86 2.67 1.61e+00 3.86e-01 2.74e+00 angle pdb=" C TYR A 116 " pdb=" N SER A 117 " pdb=" CA SER A 117 " ideal model delta sigma weight residual 122.53 119.87 2.66 1.61e+00 3.86e-01 2.73e+00 ... (remaining 4027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.48: 1404 9.48 - 18.96: 196 18.96 - 28.43: 80 28.43 - 37.91: 52 37.91 - 47.39: 20 Dihedral angle restraints: 1752 sinusoidal: 656 harmonic: 1096 Sorted by residual: dihedral pdb=" CA ILE B 26 " pdb=" C ILE B 26 " pdb=" N ASN B 27 " pdb=" CA ASN B 27 " ideal model delta harmonic sigma weight residual 180.00 161.50 18.50 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ILE E 26 " pdb=" C ILE E 26 " pdb=" N ASN E 27 " pdb=" CA ASN E 27 " ideal model delta harmonic sigma weight residual 180.00 161.51 18.49 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ILE A 26 " pdb=" C ILE A 26 " pdb=" N ASN A 27 " pdb=" CA ASN A 27 " ideal model delta harmonic sigma weight residual 180.00 161.52 18.48 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 1749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 167 0.024 - 0.048: 182 0.048 - 0.071: 56 0.071 - 0.095: 23 0.095 - 0.119: 44 Chirality restraints: 472 Sorted by residual: chirality pdb=" CA VAL E 121 " pdb=" N VAL E 121 " pdb=" C VAL E 121 " pdb=" CB VAL E 121 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.53e-01 chirality pdb=" CA ILE B 107 " pdb=" N ILE B 107 " pdb=" C ILE B 107 " pdb=" CB ILE B 107 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.45e-01 chirality pdb=" CA ILE E 107 " pdb=" N ILE E 107 " pdb=" C ILE E 107 " pdb=" CB ILE E 107 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 469 not shown) Planarity restraints: 504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 101 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO B 102 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 102 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 102 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 101 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO E 102 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO E 102 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 102 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 101 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO A 102 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " -0.035 5.00e-02 4.00e+02 ... (remaining 501 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 105 2.72 - 3.26: 2646 3.26 - 3.81: 4631 3.81 - 4.35: 5577 4.35 - 4.90: 10452 Nonbonded interactions: 23411 Sorted by model distance: nonbonded pdb=" NZ LYS C 35 " pdb=" OE2 GLU E 62 " model vdw 2.175 2.520 nonbonded pdb=" OE2 GLU A 62 " pdb=" NZ LYS B 35 " model vdw 2.192 2.520 nonbonded pdb=" NZ LYS A 35 " pdb=" OE2 GLU C 62 " model vdw 2.197 2.520 nonbonded pdb=" O SER E 85 " pdb=" OG SER E 85 " model vdw 2.305 2.440 nonbonded pdb=" O SER C 85 " pdb=" OG SER C 85 " model vdw 2.305 2.440 ... (remaining 23406 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 0.000 Extract box with map and model: 3.430 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.470 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 : 0.005 0.024 2960 Z= 0.345 Angle : 0.556 3.654 4032 Z= 0.311 Chirality : 0.048 0.119 472 Planarity : 0.006 0.063 504 Dihedral : 13.248 47.389 1040 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 11.39 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.37), residues: 356 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 79 HIS 0.001 0.000 HIS E 31 PHE 0.011 0.003 PHE B 87 TYR 0.014 0.003 TYR C 114 ARG 0.005 0.001 ARG E 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7144 (ttm-80) cc_final: 0.6864 (ttm-80) REVERT: B 89 GLU cc_start: 0.7445 (tp30) cc_final: 0.7180 (pm20) REVERT: B 103 ARG cc_start: 0.8559 (mtm180) cc_final: 0.8117 (mtm-85) REVERT: C 21 ARG cc_start: 0.7284 (ttm-80) cc_final: 0.6987 (ttm-80) REVERT: C 23 SER cc_start: 0.8760 (p) cc_final: 0.8343 (m) REVERT: C 69 TYR cc_start: 0.9063 (m-80) cc_final: 0.8265 (m-80) REVERT: E 18 ASP cc_start: 0.8298 (t0) cc_final: 0.7880 (m-30) REVERT: E 23 SER cc_start: 0.8577 (p) cc_final: 0.8258 (t) REVERT: E 72 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8220 (mt-10) REVERT: E 84 SER cc_start: 0.8072 (t) cc_final: 0.7610 (m) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.2061 time to fit residues: 16.1315 Evaluate side-chains 61 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 0.0060 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 0.0870 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 overall best weight: 0.5574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2960 Z= 0.185 Angle : 0.485 3.710 4032 Z= 0.266 Chirality : 0.047 0.116 472 Planarity : 0.005 0.043 504 Dihedral : 4.781 18.959 400 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.90 % Allowed : 12.97 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.37), residues: 356 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 79 HIS 0.001 0.000 HIS B 88 PHE 0.012 0.001 PHE A 87 TYR 0.014 0.002 TYR C 114 ARG 0.002 0.000 ARG C 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: B 21 ARG cc_start: 0.7368 (ttm-80) cc_final: 0.7079 (ttm-80) REVERT: B 103 ARG cc_start: 0.8513 (mtm180) cc_final: 0.8130 (mtm-85) REVERT: C 13 MET cc_start: 0.7455 (tpt) cc_final: 0.6899 (tmm) REVERT: C 21 ARG cc_start: 0.7244 (ttm-80) cc_final: 0.6614 (ttm-80) REVERT: C 23 SER cc_start: 0.8775 (p) cc_final: 0.8268 (m) REVERT: C 69 TYR cc_start: 0.9038 (m-80) cc_final: 0.8215 (m-80) REVERT: E 18 ASP cc_start: 0.8463 (t0) cc_final: 0.8037 (m-30) REVERT: E 21 ARG cc_start: 0.8058 (ttm-80) cc_final: 0.7310 (ttm-80) REVERT: E 23 SER cc_start: 0.8533 (p) cc_final: 0.8136 (t) REVERT: E 72 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8207 (mt-10) REVERT: E 84 SER cc_start: 0.8086 (t) cc_final: 0.7641 (m) outliers start: 6 outliers final: 5 residues processed: 62 average time/residue: 0.2531 time to fit residues: 17.6954 Evaluate side-chains 65 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain E residue 96 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2960 Z= 0.259 Angle : 0.480 3.656 4032 Z= 0.262 Chirality : 0.047 0.122 472 Planarity : 0.004 0.035 504 Dihedral : 4.755 20.143 400 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.53 % Allowed : 11.71 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.38), residues: 356 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 79 HIS 0.001 0.001 HIS C 88 PHE 0.010 0.001 PHE A 87 TYR 0.018 0.002 TYR C 114 ARG 0.004 0.001 ARG E 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: B 13 MET cc_start: 0.7633 (tpt) cc_final: 0.7326 (tpp) REVERT: B 21 ARG cc_start: 0.7390 (ttm-80) cc_final: 0.7094 (ttm-80) REVERT: B 103 ARG cc_start: 0.8513 (mtm180) cc_final: 0.8055 (mtm-85) REVERT: C 13 MET cc_start: 0.7460 (tpt) cc_final: 0.6862 (tmm) REVERT: C 21 ARG cc_start: 0.7281 (ttm-80) cc_final: 0.6600 (ttm-80) REVERT: C 23 SER cc_start: 0.8780 (p) cc_final: 0.8314 (m) REVERT: E 18 ASP cc_start: 0.8463 (t0) cc_final: 0.8051 (m-30) REVERT: E 21 ARG cc_start: 0.8079 (ttm-80) cc_final: 0.7296 (ttm-80) REVERT: E 23 SER cc_start: 0.8624 (p) cc_final: 0.8049 (t) REVERT: E 72 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8153 (mt-10) REVERT: E 84 SER cc_start: 0.8046 (t) cc_final: 0.7607 (m) REVERT: E 89 GLU cc_start: 0.7864 (tp30) cc_final: 0.7466 (tp30) outliers start: 8 outliers final: 7 residues processed: 60 average time/residue: 0.2217 time to fit residues: 15.1387 Evaluate side-chains 62 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 112 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 HIS ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2960 Z= 0.216 Angle : 0.460 3.631 4032 Z= 0.250 Chirality : 0.047 0.114 472 Planarity : 0.004 0.031 504 Dihedral : 4.603 19.455 400 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.85 % Allowed : 12.03 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.38), residues: 356 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 79 HIS 0.001 0.000 HIS C 88 PHE 0.006 0.001 PHE E 87 TYR 0.017 0.002 TYR C 114 ARG 0.004 0.000 ARG E 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.7600 (tpt) cc_final: 0.7263 (tpp) REVERT: B 13 MET cc_start: 0.7550 (tpt) cc_final: 0.7300 (tpp) REVERT: B 89 GLU cc_start: 0.7832 (tp30) cc_final: 0.7273 (pm20) REVERT: B 103 ARG cc_start: 0.8526 (mtm180) cc_final: 0.8044 (mtm-85) REVERT: C 13 MET cc_start: 0.7476 (tpt) cc_final: 0.6859 (tmm) REVERT: C 21 ARG cc_start: 0.7314 (ttm-80) cc_final: 0.6634 (ttm-80) REVERT: C 23 SER cc_start: 0.8781 (p) cc_final: 0.8282 (m) REVERT: C 89 GLU cc_start: 0.8041 (tp30) cc_final: 0.7818 (tp30) REVERT: E 18 ASP cc_start: 0.8479 (t0) cc_final: 0.8076 (m-30) REVERT: E 21 ARG cc_start: 0.8030 (ttm-80) cc_final: 0.7319 (ttm-80) REVERT: E 23 SER cc_start: 0.8625 (p) cc_final: 0.8027 (t) REVERT: E 72 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8140 (mt-10) REVERT: E 84 SER cc_start: 0.8073 (t) cc_final: 0.7600 (m) REVERT: E 89 GLU cc_start: 0.7907 (tp30) cc_final: 0.7548 (tp30) outliers start: 9 outliers final: 8 residues processed: 60 average time/residue: 0.2168 time to fit residues: 14.7632 Evaluate side-chains 63 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 112 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 17 optimal weight: 0.0270 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2960 Z= 0.282 Angle : 0.475 3.737 4032 Z= 0.258 Chirality : 0.047 0.121 472 Planarity : 0.004 0.027 504 Dihedral : 4.652 20.109 400 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.43 % Allowed : 10.44 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.38), residues: 356 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 79 HIS 0.002 0.000 HIS A 88 PHE 0.010 0.001 PHE A 87 TYR 0.016 0.002 TYR C 114 ARG 0.003 0.000 ARG E 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.7595 (tpt) cc_final: 0.7216 (tpp) REVERT: B 13 MET cc_start: 0.7549 (tpt) cc_final: 0.7336 (tpp) REVERT: B 89 GLU cc_start: 0.7880 (tp30) cc_final: 0.7352 (pm20) REVERT: C 13 MET cc_start: 0.7471 (tpt) cc_final: 0.6883 (tmm) REVERT: C 21 ARG cc_start: 0.7315 (ttm-80) cc_final: 0.6998 (ttm-80) REVERT: C 89 GLU cc_start: 0.8023 (tp30) cc_final: 0.7707 (tp30) REVERT: E 18 ASP cc_start: 0.8494 (t0) cc_final: 0.8093 (m-30) REVERT: E 23 SER cc_start: 0.8667 (p) cc_final: 0.8038 (t) REVERT: E 72 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8060 (mt-10) REVERT: E 84 SER cc_start: 0.8034 (t) cc_final: 0.7600 (m) REVERT: E 89 GLU cc_start: 0.7932 (tp30) cc_final: 0.7658 (tp30) outliers start: 14 outliers final: 10 residues processed: 66 average time/residue: 0.2395 time to fit residues: 18.0074 Evaluate side-chains 64 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 112 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2960 Z= 0.276 Angle : 0.479 3.765 4032 Z= 0.258 Chirality : 0.047 0.116 472 Planarity : 0.004 0.025 504 Dihedral : 4.641 19.872 400 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.16 % Allowed : 11.39 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.37), residues: 356 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 79 HIS 0.001 0.000 HIS A 88 PHE 0.014 0.001 PHE A 87 TYR 0.015 0.002 TYR C 114 ARG 0.007 0.001 ARG E 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.7571 (tpt) cc_final: 0.7166 (tpp) REVERT: B 13 MET cc_start: 0.7479 (tpt) cc_final: 0.7276 (tpp) REVERT: B 89 GLU cc_start: 0.7890 (tp30) cc_final: 0.7344 (pm20) REVERT: C 13 MET cc_start: 0.7448 (tpt) cc_final: 0.6906 (tmm) REVERT: C 21 ARG cc_start: 0.7356 (ttm-80) cc_final: 0.7032 (ttm-80) REVERT: C 89 GLU cc_start: 0.8097 (tp30) cc_final: 0.7736 (tp30) REVERT: E 18 ASP cc_start: 0.8479 (t0) cc_final: 0.8074 (m-30) REVERT: E 21 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7870 (ttm-80) REVERT: E 23 SER cc_start: 0.8658 (p) cc_final: 0.8048 (t) REVERT: E 34 ARG cc_start: 0.7576 (ttt180) cc_final: 0.7373 (ttt-90) REVERT: E 72 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8139 (mt-10) REVERT: E 84 SER cc_start: 0.8002 (t) cc_final: 0.7567 (m) REVERT: E 89 GLU cc_start: 0.7961 (tp30) cc_final: 0.7682 (tp30) outliers start: 10 outliers final: 9 residues processed: 63 average time/residue: 0.2317 time to fit residues: 16.5972 Evaluate side-chains 64 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 117 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2960 Z= 0.354 Angle : 0.503 3.932 4032 Z= 0.272 Chirality : 0.048 0.122 472 Planarity : 0.004 0.024 504 Dihedral : 4.764 20.311 400 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.48 % Allowed : 11.08 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.37), residues: 356 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 79 HIS 0.001 0.000 HIS A 88 PHE 0.015 0.002 PHE C 87 TYR 0.016 0.002 TYR C 114 ARG 0.005 0.001 ARG E 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.7598 (tpt) cc_final: 0.7397 (tpp) REVERT: B 13 MET cc_start: 0.7487 (tpt) cc_final: 0.7218 (tpp) REVERT: B 89 GLU cc_start: 0.7897 (tp30) cc_final: 0.7325 (pm20) REVERT: C 13 MET cc_start: 0.7418 (tpt) cc_final: 0.6919 (tmm) REVERT: C 21 ARG cc_start: 0.7400 (ttm-80) cc_final: 0.7068 (ttm-80) REVERT: C 89 GLU cc_start: 0.8114 (tp30) cc_final: 0.7781 (tp30) REVERT: E 18 ASP cc_start: 0.8481 (t0) cc_final: 0.8077 (m-30) REVERT: E 21 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7879 (ttm-80) REVERT: E 23 SER cc_start: 0.8711 (p) cc_final: 0.8103 (t) REVERT: E 34 ARG cc_start: 0.7602 (ttt180) cc_final: 0.7367 (ttt-90) REVERT: E 72 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8110 (mt-10) REVERT: E 89 GLU cc_start: 0.7931 (tp30) cc_final: 0.7048 (tm-30) outliers start: 11 outliers final: 10 residues processed: 64 average time/residue: 0.2271 time to fit residues: 16.5741 Evaluate side-chains 64 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 117 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 0.0570 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS B 90 HIS ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 2960 Z= 0.397 Angle : 0.522 4.153 4032 Z= 0.283 Chirality : 0.048 0.120 472 Planarity : 0.004 0.023 504 Dihedral : 4.867 20.485 400 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.16 % Allowed : 11.71 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.36), residues: 356 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 79 HIS 0.004 0.001 HIS B 88 PHE 0.016 0.002 PHE C 87 TYR 0.017 0.002 TYR C 114 ARG 0.004 0.001 ARG E 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.7538 (tpt) cc_final: 0.7310 (tpp) REVERT: A 69 TYR cc_start: 0.9178 (m-80) cc_final: 0.8591 (m-80) REVERT: B 13 MET cc_start: 0.7471 (tpt) cc_final: 0.7193 (tpp) REVERT: B 89 GLU cc_start: 0.7908 (tp30) cc_final: 0.7265 (pm20) REVERT: C 13 MET cc_start: 0.7426 (tpt) cc_final: 0.6946 (tmm) REVERT: C 21 ARG cc_start: 0.7423 (ttm-80) cc_final: 0.7098 (ttm-80) REVERT: C 89 GLU cc_start: 0.8144 (tp30) cc_final: 0.7796 (tp30) REVERT: C 90 HIS cc_start: 0.7995 (m90) cc_final: 0.7321 (m-70) REVERT: E 18 ASP cc_start: 0.8454 (t0) cc_final: 0.8040 (m-30) REVERT: E 21 ARG cc_start: 0.8139 (ttm-80) cc_final: 0.7886 (ttm-80) REVERT: E 23 SER cc_start: 0.8742 (p) cc_final: 0.8120 (t) REVERT: E 72 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8100 (mt-10) REVERT: E 89 GLU cc_start: 0.7927 (tp30) cc_final: 0.7060 (tm-30) outliers start: 10 outliers final: 10 residues processed: 63 average time/residue: 0.2160 time to fit residues: 15.5950 Evaluate side-chains 66 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 117 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2960 Z= 0.253 Angle : 0.469 3.654 4032 Z= 0.255 Chirality : 0.047 0.116 472 Planarity : 0.004 0.024 504 Dihedral : 4.652 19.618 400 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.16 % Allowed : 12.03 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.37), residues: 356 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 79 HIS 0.002 0.000 HIS A 88 PHE 0.010 0.001 PHE A 87 TYR 0.016 0.002 TYR C 114 ARG 0.004 0.001 ARG E 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.7495 (tpt) cc_final: 0.7253 (tpp) REVERT: B 13 MET cc_start: 0.7444 (tpt) cc_final: 0.7193 (tpp) REVERT: B 89 GLU cc_start: 0.7944 (tp30) cc_final: 0.7370 (pm20) REVERT: C 13 MET cc_start: 0.7425 (tpt) cc_final: 0.6948 (tmm) REVERT: C 21 ARG cc_start: 0.7449 (ttm-80) cc_final: 0.7122 (ttm-80) REVERT: C 89 GLU cc_start: 0.8179 (tp30) cc_final: 0.7848 (tp30) REVERT: C 90 HIS cc_start: 0.8036 (m90) cc_final: 0.7377 (m-70) REVERT: E 18 ASP cc_start: 0.8452 (t0) cc_final: 0.8043 (m-30) REVERT: E 21 ARG cc_start: 0.8138 (ttm-80) cc_final: 0.7893 (ttm-80) REVERT: E 23 SER cc_start: 0.8765 (p) cc_final: 0.8173 (t) REVERT: E 72 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8091 (mt-10) REVERT: E 89 GLU cc_start: 0.7949 (tp30) cc_final: 0.7170 (tm-30) outliers start: 10 outliers final: 10 residues processed: 62 average time/residue: 0.2186 time to fit residues: 15.4762 Evaluate side-chains 64 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2960 Z= 0.228 Angle : 0.461 3.604 4032 Z= 0.250 Chirality : 0.047 0.119 472 Planarity : 0.004 0.036 504 Dihedral : 4.563 19.458 400 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.22 % Allowed : 13.61 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.37), residues: 356 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 79 HIS 0.001 0.000 HIS A 88 PHE 0.009 0.001 PHE A 87 TYR 0.015 0.002 TYR C 114 ARG 0.009 0.001 ARG E 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.7475 (tpt) cc_final: 0.7232 (tpp) REVERT: B 13 MET cc_start: 0.7383 (tpt) cc_final: 0.7128 (tpp) REVERT: B 89 GLU cc_start: 0.7952 (tp30) cc_final: 0.7363 (pm20) REVERT: C 13 MET cc_start: 0.7429 (tpt) cc_final: 0.6962 (tmm) REVERT: C 21 ARG cc_start: 0.7463 (ttm-80) cc_final: 0.7139 (ttm-80) REVERT: C 35 LYS cc_start: 0.8202 (ttmm) cc_final: 0.7923 (tttm) REVERT: C 89 GLU cc_start: 0.8185 (tp30) cc_final: 0.7824 (tp30) REVERT: E 18 ASP cc_start: 0.8436 (t0) cc_final: 0.8023 (m-30) REVERT: E 21 ARG cc_start: 0.8138 (ttm-80) cc_final: 0.7919 (ttm-80) REVERT: E 23 SER cc_start: 0.8752 (p) cc_final: 0.8127 (t) REVERT: E 72 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8090 (mt-10) REVERT: E 89 GLU cc_start: 0.7956 (tp30) cc_final: 0.7163 (tm-30) outliers start: 7 outliers final: 7 residues processed: 61 average time/residue: 0.2336 time to fit residues: 16.1498 Evaluate side-chains 63 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.147607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.115449 restraints weight = 3566.208| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 3.15 r_work: 0.3784 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 2960 Z= 0.425 Angle : 0.542 4.300 4032 Z= 0.295 Chirality : 0.048 0.124 472 Planarity : 0.004 0.039 504 Dihedral : 4.886 20.784 400 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.53 % Allowed : 13.61 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.36), residues: 356 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 79 HIS 0.002 0.001 HIS A 88 PHE 0.010 0.002 PHE A 87 TYR 0.017 0.002 TYR C 114 ARG 0.007 0.001 ARG E 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1261.15 seconds wall clock time: 23 minutes 20.60 seconds (1400.60 seconds total)