Starting phenix.real_space_refine on Sat Jul 20 23:55:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txw_41707/07_2024/8txw_41707.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txw_41707/07_2024/8txw_41707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txw_41707/07_2024/8txw_41707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txw_41707/07_2024/8txw_41707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txw_41707/07_2024/8txw_41707.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txw_41707/07_2024/8txw_41707.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 15 5.16 5 C 7144 2.51 5 N 2407 2.21 5 O 2975 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "D ASP 51": "OD1" <-> "OD2" Residue "D TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E ASP 106": "OD1" <-> "OD2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 68": "OD1" <-> "OD2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "K GLU 473": "OE1" <-> "OE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 64": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 12835 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "H" Number of atoms: 743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 728 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 117 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "M" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Time building chain proxies: 7.26, per 1000 atoms: 0.57 Number of scatterers: 12835 At special positions: 0 Unit cell: (103.584, 124.832, 119.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 294 15.00 O 2975 8.00 N 2407 7.00 C 7144 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: 6.08 Conformation dependent library (CDL) restraints added in 1.5 seconds 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1600 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 11 sheets defined 67.6% alpha, 4.2% beta 135 base pairs and 242 stacking pairs defined. Time for finding SS restraints: 5.95 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.534A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.814A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.768A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.516A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.559A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.618A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.741A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.876A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.624A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.737A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.681A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'M' and resid 37 through 41 Processing helix chain 'M' and resid 55 through 60 removed outlier: 4.482A pdb=" N TYR M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.987A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.767A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.509A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.124A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'F' and resid 97 through 98 Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54 removed outlier: 7.395A pdb=" N GLY H 53 " --> pdb=" O ILE G 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AB2, first strand: chain 'M' and resid 12 through 16 removed outlier: 9.254A pdb=" N LEU M 67 " --> pdb=" O GLN M 2 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N PHE M 4 " --> pdb=" O LEU M 67 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEU M 69 " --> pdb=" O PHE M 4 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS M 6 " --> pdb=" O LEU M 69 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS M 68 " --> pdb=" O ILE M 44 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1237 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 348 hydrogen bonds 692 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 242 stacking parallelities Total time for adding SS restraints: 4.66 Time building geometry restraints manager: 6.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2641 1.33 - 1.45: 4217 1.45 - 1.57: 6188 1.57 - 1.69: 586 1.69 - 1.81: 26 Bond restraints: 13658 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.452 -0.030 3.00e-02 1.11e+03 9.75e-01 bond pdb=" CB GLU H 93 " pdb=" CG GLU H 93 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.54e-01 bond pdb=" C3' DG J 21 " pdb=" C2' DG J 21 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 8.08e-01 bond pdb=" C3' DA J -68 " pdb=" C2' DA J -68 " ideal model delta sigma weight residual 1.525 1.542 -0.017 2.00e-02 2.50e+03 7.45e-01 bond pdb=" C4' DG I 26 " pdb=" C3' DG I 26 " ideal model delta sigma weight residual 1.523 1.506 0.017 2.00e-02 2.50e+03 7.41e-01 ... (remaining 13653 not shown) Histogram of bond angle deviations from ideal: 98.73 - 105.47: 1352 105.47 - 112.21: 7556 112.21 - 118.96: 3374 118.96 - 125.70: 6420 125.70 - 132.44: 994 Bond angle restraints: 19696 Sorted by residual: angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 121.54 127.95 -6.41 1.91e+00 2.74e-01 1.13e+01 angle pdb=" C GLU K 473 " pdb=" N TYR K 474 " pdb=" CA TYR K 474 " ideal model delta sigma weight residual 121.54 127.42 -5.88 1.91e+00 2.74e-01 9.47e+00 angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 113.18 119.82 -6.64 2.37e+00 1.78e-01 7.86e+00 angle pdb=" CA GLU A 105 " pdb=" CB GLU A 105 " pdb=" CG GLU A 105 " ideal model delta sigma weight residual 114.10 118.83 -4.73 2.00e+00 2.50e-01 5.60e+00 angle pdb=" CB MET H 59 " pdb=" CG MET H 59 " pdb=" SD MET H 59 " ideal model delta sigma weight residual 112.70 118.98 -6.28 3.00e+00 1.11e-01 4.39e+00 ... (remaining 19691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.97: 5846 29.97 - 59.94: 1584 59.94 - 89.91: 58 89.91 - 119.88: 0 119.88 - 149.84: 2 Dihedral angle restraints: 7490 sinusoidal: 5007 harmonic: 2483 Sorted by residual: dihedral pdb=" CA LYS G 15 " pdb=" C LYS G 15 " pdb=" N THR G 16 " pdb=" CA THR G 16 " ideal model delta harmonic sigma weight residual 180.00 159.47 20.53 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual -180.00 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 70.16 149.84 1 3.50e+01 8.16e-04 1.46e+01 ... (remaining 7487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1617 0.031 - 0.062: 490 0.062 - 0.094: 87 0.094 - 0.125: 42 0.125 - 0.156: 4 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.07e-01 chirality pdb=" CA GLU H 93 " pdb=" N GLU H 93 " pdb=" C GLU H 93 " pdb=" CB GLU H 93 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CB ILE M 36 " pdb=" CA ILE M 36 " pdb=" CG1 ILE M 36 " pdb=" CG2 ILE M 36 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 2237 not shown) Planarity restraints: 1477 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 88 " 0.016 2.00e-02 2.50e+03 2.12e-02 8.95e+00 pdb=" CG TYR F 88 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR F 88 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR F 88 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR F 88 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR F 88 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR F 88 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 88 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 83 " 0.007 2.00e-02 2.50e+03 1.60e-02 5.11e+00 pdb=" CG TYR H 83 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR H 83 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR H 83 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR H 83 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR H 83 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR H 83 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 83 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 83 " 0.017 2.00e-02 2.50e+03 1.15e-02 2.66e+00 pdb=" CG TYR D 83 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR D 83 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR D 83 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 83 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 83 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR D 83 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR D 83 " 0.001 2.00e-02 2.50e+03 ... (remaining 1474 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1691 2.76 - 3.47: 17243 3.47 - 4.19: 34381 4.19 - 4.90: 52658 Nonbonded interactions: 105975 Sorted by model distance: nonbonded pdb=" C SER H 123 " pdb=" N SER G 11 " model vdw 1.328 3.350 nonbonded pdb=" C SER D 123 " pdb=" N SER C 11 " model vdw 1.331 3.350 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.123 2.496 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.203 2.440 nonbonded pdb=" O SER D 123 " pdb=" N SER C 11 " model vdw 2.246 2.520 ... (remaining 105970 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 40.630 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 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 : 0.004 0.030 13658 Z= 0.198 Angle : 0.542 6.643 19696 Z= 0.325 Chirality : 0.033 0.156 2240 Planarity : 0.004 0.038 1477 Dihedral : 26.877 149.845 5890 Min Nonbonded Distance : 1.328 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.14 % Allowed : 0.00 % Favored : 99.86 % 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: 2.65 (0.29), residues: 839 helix: 2.90 (0.22), residues: 545 sheet: 0.77 (1.24), residues: 20 loop : -0.61 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 82 PHE 0.007 0.001 PHE A 67 TYR 0.052 0.002 TYR F 88 ARG 0.008 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: A 110 CYS cc_start: 0.8593 (t) cc_final: 0.7673 (t) REVERT: A 123 ASP cc_start: 0.9036 (m-30) cc_final: 0.8103 (m-30) REVERT: D 71 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8248 (tm-30) REVERT: E 123 ASP cc_start: 0.9098 (m-30) cc_final: 0.8838 (m-30) REVERT: E 129 ARG cc_start: 0.8548 (tpt90) cc_final: 0.8099 (tpt90) REVERT: F 85 ASP cc_start: 0.8813 (m-30) cc_final: 0.8565 (m-30) REVERT: H 85 LYS cc_start: 0.9321 (mttm) cc_final: 0.9035 (mmtt) REVERT: H 99 ARG cc_start: 0.8516 (mtt-85) cc_final: 0.8278 (mtm-85) REVERT: H 120 LYS cc_start: 0.9214 (tttm) cc_final: 0.9008 (tttp) REVERT: C 40 SER cc_start: 0.8899 (t) cc_final: 0.8695 (t) REVERT: C 95 LYS cc_start: 0.9191 (tptm) cc_final: 0.8814 (ttmm) REVERT: G 41 GLU cc_start: 0.8591 (tp30) cc_final: 0.8376 (tp30) REVERT: G 64 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8415 (tm-30) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.3303 time to fit residues: 77.1472 Evaluate side-chains 152 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 0.0970 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 93 GLN A 108 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 13658 Z= 0.383 Angle : 0.618 7.670 19696 Z= 0.365 Chirality : 0.037 0.193 2240 Planarity : 0.004 0.036 1477 Dihedral : 29.835 150.617 4170 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.25 % Allowed : 9.85 % Favored : 88.90 % 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: 2.43 (0.30), residues: 839 helix: 2.68 (0.22), residues: 560 sheet: 0.20 (1.14), residues: 20 loop : -0.74 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.010 0.002 PHE B 61 TYR 0.049 0.002 TYR F 88 ARG 0.007 0.001 ARG F 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 158 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 110 CYS cc_start: 0.8486 (t) cc_final: 0.7824 (t) REVERT: A 123 ASP cc_start: 0.9245 (m-30) cc_final: 0.8568 (m-30) REVERT: B 88 TYR cc_start: 0.8839 (m-10) cc_final: 0.8138 (m-10) REVERT: D 85 LYS cc_start: 0.9325 (mtpp) cc_final: 0.9110 (mtpp) REVERT: D 99 ARG cc_start: 0.9007 (tpp80) cc_final: 0.8659 (ttm-80) REVERT: E 120 MET cc_start: 0.8396 (mtt) cc_final: 0.8180 (mtt) REVERT: E 122 LYS cc_start: 0.8895 (ptpp) cc_final: 0.8608 (ptpp) REVERT: E 123 ASP cc_start: 0.9056 (m-30) cc_final: 0.8820 (m-30) REVERT: E 129 ARG cc_start: 0.8626 (tpt90) cc_final: 0.8162 (tpt90) REVERT: F 85 ASP cc_start: 0.8784 (m-30) cc_final: 0.8549 (m-30) REVERT: H 85 LYS cc_start: 0.9353 (mttm) cc_final: 0.9036 (mmtt) REVERT: H 120 LYS cc_start: 0.9297 (tttm) cc_final: 0.9051 (tttp) REVERT: C 95 LYS cc_start: 0.9221 (tptm) cc_final: 0.8887 (ttmm) REVERT: G 64 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8789 (tm-30) outliers start: 8 outliers final: 7 residues processed: 162 average time/residue: 0.3374 time to fit residues: 72.0672 Evaluate side-chains 153 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 146 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN F 25 ASN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 13658 Z= 0.370 Angle : 0.609 7.220 19696 Z= 0.360 Chirality : 0.037 0.176 2240 Planarity : 0.004 0.033 1477 Dihedral : 29.901 149.796 4170 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.80 % Allowed : 13.31 % Favored : 84.88 % 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: 2.22 (0.29), residues: 839 helix: 2.57 (0.22), residues: 559 sheet: -0.19 (1.12), residues: 20 loop : -0.94 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.009 0.002 PHE A 67 TYR 0.039 0.002 TYR F 88 ARG 0.005 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 153 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8889 (m-10) cc_final: 0.8067 (m-80) REVERT: D 71 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8221 (tp30) REVERT: D 85 LYS cc_start: 0.9336 (mtpp) cc_final: 0.9134 (mtpp) REVERT: D 99 ARG cc_start: 0.8991 (tpp80) cc_final: 0.8645 (ttm-80) REVERT: E 129 ARG cc_start: 0.8578 (tpt90) cc_final: 0.8111 (tpt90) REVERT: F 85 ASP cc_start: 0.8774 (m-30) cc_final: 0.8524 (m-30) REVERT: H 85 LYS cc_start: 0.9370 (mttm) cc_final: 0.9040 (mmtt) REVERT: H 120 LYS cc_start: 0.9305 (tttm) cc_final: 0.9066 (tttp) REVERT: C 39 TYR cc_start: 0.9331 (m-80) cc_final: 0.8954 (m-80) REVERT: C 95 LYS cc_start: 0.9252 (tptm) cc_final: 0.8883 (ttmm) REVERT: G 64 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8761 (tm-30) outliers start: 12 outliers final: 10 residues processed: 159 average time/residue: 0.3351 time to fit residues: 70.2777 Evaluate side-chains 159 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 111 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN E 68 GLN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13658 Z= 0.191 Angle : 0.545 7.137 19696 Z= 0.327 Chirality : 0.033 0.176 2240 Planarity : 0.004 0.035 1477 Dihedral : 29.692 149.167 4170 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.27 % Favored : 97.61 % Rotamer: Outliers : 1.94 % Allowed : 14.01 % Favored : 84.05 % 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: 2.58 (0.30), residues: 839 helix: 2.88 (0.22), residues: 557 sheet: -0.01 (1.12), residues: 20 loop : -0.85 (0.35), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 49 PHE 0.006 0.001 PHE A 67 TYR 0.032 0.001 TYR F 88 ARG 0.005 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 152 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8612 (pm20) cc_final: 0.8325 (pm20) REVERT: B 88 TYR cc_start: 0.8842 (m-10) cc_final: 0.8110 (m-80) REVERT: D 71 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8380 (tp30) REVERT: D 85 LYS cc_start: 0.9334 (mtpp) cc_final: 0.9127 (mtpp) REVERT: D 99 ARG cc_start: 0.8959 (tpp80) cc_final: 0.8591 (ttm-80) REVERT: E 122 LYS cc_start: 0.8827 (ptpp) cc_final: 0.8513 (ptpp) REVERT: E 123 ASP cc_start: 0.9085 (m-30) cc_final: 0.8824 (m-30) REVERT: E 129 ARG cc_start: 0.8561 (tpt90) cc_final: 0.8139 (tpt90) REVERT: F 85 ASP cc_start: 0.8758 (m-30) cc_final: 0.8502 (m-30) REVERT: H 85 LYS cc_start: 0.9369 (mttm) cc_final: 0.9052 (mmtt) REVERT: H 120 LYS cc_start: 0.9357 (tttm) cc_final: 0.9132 (tttp) REVERT: C 15 LYS cc_start: 0.7656 (ptpp) cc_final: 0.7322 (pttm) REVERT: C 39 TYR cc_start: 0.9285 (m-80) cc_final: 0.8944 (m-80) REVERT: C 95 LYS cc_start: 0.9222 (tptm) cc_final: 0.8894 (ttmm) REVERT: G 64 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8370 (tt0) outliers start: 13 outliers final: 10 residues processed: 157 average time/residue: 0.3355 time to fit residues: 69.6908 Evaluate side-chains 159 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.0870 chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 13658 Z= 0.449 Angle : 0.647 7.426 19696 Z= 0.379 Chirality : 0.039 0.184 2240 Planarity : 0.004 0.035 1477 Dihedral : 30.066 150.022 4170 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.11 % Favored : 96.77 % Rotamer: Outliers : 2.08 % Allowed : 16.23 % Favored : 81.69 % 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: 2.12 (0.30), residues: 839 helix: 2.54 (0.22), residues: 560 sheet: -0.46 (1.13), residues: 20 loop : -1.09 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.011 0.002 PHE B 61 TYR 0.045 0.002 TYR F 88 ARG 0.006 0.001 ARG F 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 154 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8691 (pm20) cc_final: 0.8350 (pm20) REVERT: B 88 TYR cc_start: 0.8939 (m-10) cc_final: 0.8086 (m-80) REVERT: D 71 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8143 (tp30) REVERT: D 99 ARG cc_start: 0.9017 (tpp80) cc_final: 0.8644 (ttm-80) REVERT: D 121 TYR cc_start: 0.9150 (t80) cc_final: 0.8905 (t80) REVERT: E 129 ARG cc_start: 0.8583 (tpt90) cc_final: 0.8080 (tpt90) REVERT: F 85 ASP cc_start: 0.8778 (m-30) cc_final: 0.8539 (m-30) REVERT: H 85 LYS cc_start: 0.9374 (mttm) cc_final: 0.9057 (mmtt) REVERT: C 39 TYR cc_start: 0.9373 (m-80) cc_final: 0.8984 (m-80) REVERT: C 95 LYS cc_start: 0.9199 (tptm) cc_final: 0.8848 (ttmm) REVERT: G 64 GLU cc_start: 0.8985 (tm-30) cc_final: 0.8738 (tm-30) outliers start: 14 outliers final: 11 residues processed: 161 average time/residue: 0.3261 time to fit residues: 69.9231 Evaluate side-chains 162 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 151 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13658 Z= 0.199 Angle : 0.552 9.090 19696 Z= 0.329 Chirality : 0.033 0.169 2240 Planarity : 0.004 0.036 1477 Dihedral : 29.801 149.151 4170 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.15 % Favored : 97.73 % Rotamer: Outliers : 1.53 % Allowed : 17.06 % Favored : 81.41 % 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: 2.52 (0.30), residues: 839 helix: 2.88 (0.22), residues: 557 sheet: -0.09 (1.18), residues: 20 loop : -0.99 (0.35), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 49 PHE 0.007 0.001 PHE A 78 TYR 0.023 0.001 TYR F 88 ARG 0.007 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 155 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8649 (pm20) cc_final: 0.8277 (pm20) REVERT: B 88 TYR cc_start: 0.8908 (m-10) cc_final: 0.8221 (m-10) REVERT: D 71 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8388 (tp30) REVERT: D 99 ARG cc_start: 0.8970 (tpp80) cc_final: 0.8593 (ttm-80) REVERT: E 123 ASP cc_start: 0.9094 (m-30) cc_final: 0.8827 (m-30) REVERT: E 129 ARG cc_start: 0.8545 (tpt90) cc_final: 0.8116 (tpt90) REVERT: F 85 ASP cc_start: 0.8745 (m-30) cc_final: 0.8485 (m-30) REVERT: H 85 LYS cc_start: 0.9370 (mttm) cc_final: 0.9034 (mmtt) REVERT: C 15 LYS cc_start: 0.7599 (ptpp) cc_final: 0.7203 (ptpp) REVERT: C 39 TYR cc_start: 0.9321 (m-80) cc_final: 0.8986 (m-80) REVERT: C 95 LYS cc_start: 0.9170 (tptm) cc_final: 0.8879 (ttmm) REVERT: G 64 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8697 (tm-30) outliers start: 10 outliers final: 8 residues processed: 160 average time/residue: 0.3227 time to fit residues: 68.7820 Evaluate side-chains 159 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 151 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN E 68 GLN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.063 13658 Z= 0.550 Angle : 0.707 9.912 19696 Z= 0.408 Chirality : 0.043 0.166 2240 Planarity : 0.005 0.034 1477 Dihedral : 30.264 150.412 4170 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.23 % Favored : 96.54 % Rotamer: Outliers : 1.94 % Allowed : 17.34 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.29), residues: 839 helix: 2.36 (0.22), residues: 560 sheet: -0.58 (1.20), residues: 20 loop : -1.31 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 49 PHE 0.012 0.002 PHE B 61 TYR 0.042 0.003 TYR F 88 ARG 0.005 0.001 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 152 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8798 (pm20) cc_final: 0.8426 (pm20) REVERT: B 88 TYR cc_start: 0.8915 (m-10) cc_final: 0.8049 (m-80) REVERT: D 35 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8352 (mt-10) REVERT: D 71 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8137 (tp30) REVERT: E 129 ARG cc_start: 0.8630 (tpt90) cc_final: 0.8101 (tpt90) REVERT: F 85 ASP cc_start: 0.8784 (m-30) cc_final: 0.8546 (m-30) REVERT: H 85 LYS cc_start: 0.9370 (mttm) cc_final: 0.9035 (mmtt) REVERT: C 39 TYR cc_start: 0.9440 (m-80) cc_final: 0.9065 (m-80) REVERT: C 95 LYS cc_start: 0.9207 (tptm) cc_final: 0.8843 (ttmm) REVERT: G 64 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8751 (tm-30) outliers start: 13 outliers final: 12 residues processed: 159 average time/residue: 0.3151 time to fit residues: 66.7021 Evaluate side-chains 163 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 151 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN E 68 GLN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13658 Z= 0.222 Angle : 0.573 10.979 19696 Z= 0.339 Chirality : 0.034 0.188 2240 Planarity : 0.004 0.036 1477 Dihedral : 29.901 149.170 4170 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.03 % Favored : 97.73 % Rotamer: Outliers : 1.53 % Allowed : 18.31 % Favored : 80.17 % 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: 2.36 (0.30), residues: 839 helix: 2.81 (0.22), residues: 557 sheet: -0.30 (1.24), residues: 20 loop : -1.17 (0.35), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.007 0.001 PHE E 78 TYR 0.025 0.002 TYR F 88 ARG 0.006 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 158 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8662 (pm20) cc_final: 0.8244 (pm20) REVERT: B 88 TYR cc_start: 0.8942 (m-10) cc_final: 0.8282 (m-10) REVERT: D 71 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8294 (tp30) REVERT: D 99 ARG cc_start: 0.8956 (tpp80) cc_final: 0.8569 (ttm-80) REVERT: E 129 ARG cc_start: 0.8542 (tpt90) cc_final: 0.8078 (tpt90) REVERT: F 85 ASP cc_start: 0.8759 (m-30) cc_final: 0.8516 (m-30) REVERT: H 85 LYS cc_start: 0.9348 (mttm) cc_final: 0.9028 (mmtt) REVERT: C 15 LYS cc_start: 0.7522 (ptpp) cc_final: 0.7116 (ptpp) REVERT: C 39 TYR cc_start: 0.9371 (m-80) cc_final: 0.9001 (m-80) REVERT: C 95 LYS cc_start: 0.9189 (tptm) cc_final: 0.8832 (ttmm) REVERT: G 64 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8695 (tm-30) outliers start: 10 outliers final: 9 residues processed: 164 average time/residue: 0.3318 time to fit residues: 72.3292 Evaluate side-chains 162 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 153 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 0.0770 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 91 optimal weight: 0.0980 chunk 96 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 93 GLN D 47 GLN E 68 GLN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13658 Z= 0.176 Angle : 0.553 11.247 19696 Z= 0.327 Chirality : 0.032 0.166 2240 Planarity : 0.004 0.037 1477 Dihedral : 29.638 149.766 4170 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.51 % Favored : 97.37 % Rotamer: Outliers : 1.39 % Allowed : 18.45 % Favored : 80.17 % 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: 2.57 (0.29), residues: 839 helix: 2.93 (0.22), residues: 558 sheet: 0.05 (1.23), residues: 20 loop : -1.04 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 82 PHE 0.008 0.001 PHE A 78 TYR 0.014 0.001 TYR F 98 ARG 0.006 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 175 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8610 (pm20) cc_final: 0.8205 (pm20) REVERT: B 88 TYR cc_start: 0.8948 (m-10) cc_final: 0.8362 (m-10) REVERT: D 71 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8398 (tp30) REVERT: E 129 ARG cc_start: 0.8518 (tpt90) cc_final: 0.8095 (tpt90) REVERT: F 85 ASP cc_start: 0.8668 (m-30) cc_final: 0.8442 (m-30) REVERT: H 85 LYS cc_start: 0.9335 (mttm) cc_final: 0.9008 (mmtt) REVERT: C 15 LYS cc_start: 0.7365 (ptpp) cc_final: 0.7091 (pttm) REVERT: C 39 TYR cc_start: 0.9259 (m-80) cc_final: 0.8992 (m-80) REVERT: C 95 LYS cc_start: 0.9232 (tptm) cc_final: 0.8881 (ttmm) REVERT: G 64 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8458 (tm-30) outliers start: 9 outliers final: 6 residues processed: 181 average time/residue: 0.3172 time to fit residues: 76.7166 Evaluate side-chains 168 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 162 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN F 25 ASN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13658 Z= 0.282 Angle : 0.595 12.281 19696 Z= 0.346 Chirality : 0.035 0.174 2240 Planarity : 0.004 0.036 1477 Dihedral : 29.821 150.882 4170 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.11 % Favored : 96.77 % Rotamer: Outliers : 0.97 % Allowed : 19.56 % Favored : 79.47 % 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: 2.49 (0.30), residues: 839 helix: 2.88 (0.22), residues: 558 sheet: -0.11 (1.22), residues: 20 loop : -1.08 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 49 PHE 0.008 0.001 PHE B 61 TYR 0.040 0.002 TYR F 88 ARG 0.006 0.000 ARG D 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 158 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8591 (pm20) cc_final: 0.8160 (pm20) REVERT: A 123 ASP cc_start: 0.9075 (m-30) cc_final: 0.8766 (m-30) REVERT: B 88 TYR cc_start: 0.8898 (m-10) cc_final: 0.8193 (m-10) REVERT: D 71 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8277 (tp30) REVERT: D 99 ARG cc_start: 0.8991 (tpp80) cc_final: 0.8571 (ttm-80) REVERT: E 129 ARG cc_start: 0.8521 (tpt90) cc_final: 0.8061 (tpt90) REVERT: F 85 ASP cc_start: 0.8719 (m-30) cc_final: 0.8468 (m-30) REVERT: H 85 LYS cc_start: 0.9334 (mttm) cc_final: 0.9031 (mmtt) REVERT: C 15 LYS cc_start: 0.7502 (ptpp) cc_final: 0.7188 (pttm) REVERT: C 39 TYR cc_start: 0.9317 (m-80) cc_final: 0.8989 (m-80) REVERT: C 95 LYS cc_start: 0.9215 (tptm) cc_final: 0.8817 (ttmm) REVERT: G 64 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8762 (tm-30) outliers start: 6 outliers final: 5 residues processed: 161 average time/residue: 0.3217 time to fit residues: 68.4732 Evaluate side-chains 162 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 157 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 85 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** 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 = 0.3555 r_free = 0.3555 target = 0.103982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.068119 restraints weight = 40300.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.070523 restraints weight = 18832.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.072160 restraints weight = 12514.211| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13658 Z= 0.197 Angle : 0.567 11.849 19696 Z= 0.332 Chirality : 0.033 0.171 2240 Planarity : 0.004 0.036 1477 Dihedral : 29.740 150.087 4170 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.51 % Favored : 97.37 % Rotamer: Outliers : 0.97 % Allowed : 19.42 % Favored : 79.61 % 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: 2.54 (0.30), residues: 839 helix: 2.91 (0.22), residues: 558 sheet: -0.05 (1.21), residues: 20 loop : -1.05 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 49 PHE 0.007 0.001 PHE E 67 TYR 0.030 0.001 TYR F 88 ARG 0.007 0.000 ARG D 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2263.49 seconds wall clock time: 41 minutes 4.94 seconds (2464.94 seconds total)