Starting phenix.real_space_refine on Mon Aug 5 05:38:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txw_41707/08_2024/8txw_41707.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txw_41707/08_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_41707/08_2024/8txw_41707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txw_41707/08_2024/8txw_41707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txw_41707/08_2024/8txw_41707.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txw_41707/08_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-5409/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: 7.48, per 1000 atoms: 0.58 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: 6.36 Conformation dependent library (CDL) restraints added in 1.6 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: 5.82 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: 4.80 Time building geometry restraints manager: 6.85 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 3.040 nonbonded pdb=" O SER D 123 " pdb=" N SER C 11 " model vdw 2.246 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 1.100 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 41.040 Find NCS groups from input model: 0.270 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: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.030 ------------------------------------------------------------------------------- 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 : 0.977 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: 0.3411 time to fit residues: 80.0805 Evaluate side-chains 152 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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: 0.9980 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13658 Z= 0.299 Angle : 0.585 7.594 19696 Z= 0.347 Chirality : 0.036 0.188 2240 Planarity : 0.004 0.036 1477 Dihedral : 29.751 150.364 4170 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.97 % Allowed : 9.15 % Favored : 89.88 % 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: 2.57 (0.30), residues: 839 helix: 2.76 (0.22), residues: 561 sheet: 0.28 (1.18), residues: 20 loop : -0.65 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 49 PHE 0.009 0.002 PHE A 67 TYR 0.044 0.003 TYR F 88 ARG 0.005 0.000 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 171 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 165 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 CYS cc_start: 0.8597 (t) cc_final: 0.7805 (t) REVERT: A 123 ASP cc_start: 0.9256 (m-30) cc_final: 0.8595 (m-30) REVERT: B 88 TYR cc_start: 0.8814 (m-10) cc_final: 0.8019 (m-10) REVERT: D 71 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8266 (tm-30) REVERT: D 85 LYS cc_start: 0.9318 (mtpp) cc_final: 0.9103 (mtpp) REVERT: E 120 MET cc_start: 0.8224 (mtt) cc_final: 0.8015 (mtt) REVERT: E 122 LYS cc_start: 0.8838 (ptpp) cc_final: 0.8584 (ptpp) REVERT: E 123 ASP cc_start: 0.9127 (m-30) cc_final: 0.8879 (m-30) REVERT: E 129 ARG cc_start: 0.8612 (tpt90) cc_final: 0.8164 (tpt90) REVERT: F 85 ASP cc_start: 0.8775 (m-30) cc_final: 0.8515 (m-30) REVERT: H 85 LYS cc_start: 0.9344 (mttm) cc_final: 0.9025 (mmtt) REVERT: H 120 LYS cc_start: 0.9301 (tttm) cc_final: 0.9073 (tttp) REVERT: C 95 LYS cc_start: 0.9295 (tptm) cc_final: 0.9001 (ttmm) REVERT: G 64 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8755 (tm-30) outliers start: 6 outliers final: 6 residues processed: 167 average time/residue: 0.3268 time to fit residues: 72.0042 Evaluate side-chains 155 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 149 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 30 optimal weight: 0.8980 chunk 81 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13658 Z= 0.278 Angle : 0.570 8.014 19696 Z= 0.339 Chirality : 0.035 0.183 2240 Planarity : 0.004 0.034 1477 Dihedral : 29.739 149.651 4170 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.39 % Allowed : 13.04 % Favored : 85.58 % 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: 2.51 (0.30), residues: 839 helix: 2.76 (0.22), residues: 560 sheet: 0.18 (1.17), residues: 20 loop : -0.76 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 49 PHE 0.009 0.001 PHE A 67 TYR 0.032 0.002 TYR F 88 ARG 0.006 0.000 ARG F 23 *********************** 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 157 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 148 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8720 (pm20) cc_final: 0.8296 (pm20) REVERT: A 76 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8609 (tm-30) REVERT: B 88 TYR cc_start: 0.8855 (m-10) cc_final: 0.8116 (m-10) REVERT: D 71 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8362 (tp30) REVERT: D 99 ARG cc_start: 0.8979 (tpp80) cc_final: 0.8621 (ttm-80) REVERT: E 120 MET cc_start: 0.8303 (mtt) cc_final: 0.8068 (mtt) REVERT: E 123 ASP cc_start: 0.9186 (m-30) cc_final: 0.8971 (m-30) REVERT: E 129 ARG cc_start: 0.8601 (tpt90) cc_final: 0.8152 (tpt90) REVERT: F 85 ASP cc_start: 0.8786 (m-30) cc_final: 0.8522 (m-30) REVERT: H 85 LYS cc_start: 0.9355 (mttm) cc_final: 0.9029 (mmtt) REVERT: H 120 LYS cc_start: 0.9276 (tttm) cc_final: 0.9043 (tttp) REVERT: C 15 LYS cc_start: 0.7761 (ptpp) cc_final: 0.7532 (pttm) REVERT: C 95 LYS cc_start: 0.9231 (tptm) cc_final: 0.8898 (ttmm) outliers start: 9 outliers final: 8 residues processed: 152 average time/residue: 0.3253 time to fit residues: 66.1187 Evaluate side-chains 155 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 147 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 118 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8602 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13658 Z= 0.207 Angle : 0.547 7.329 19696 Z= 0.326 Chirality : 0.033 0.183 2240 Planarity : 0.004 0.034 1477 Dihedral : 29.662 149.422 4170 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.39 % Favored : 97.49 % Rotamer: Outliers : 1.39 % Allowed : 14.29 % Favored : 84.33 % 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: 2.62 (0.29), residues: 839 helix: 2.86 (0.22), residues: 560 sheet: 0.44 (1.20), residues: 20 loop : -0.79 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.031 0.002 TYR F 88 ARG 0.006 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 164 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 155 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8756 (pm20) cc_final: 0.8243 (pm20) REVERT: A 76 GLN cc_start: 0.8795 (tm-30) cc_final: 0.8537 (tm-30) REVERT: B 88 TYR cc_start: 0.8882 (m-10) cc_final: 0.8339 (m-10) REVERT: D 71 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8371 (tp30) REVERT: E 120 MET cc_start: 0.8192 (mtt) cc_final: 0.7901 (mtt) REVERT: E 122 LYS cc_start: 0.8804 (ptpp) cc_final: 0.8541 (ptpp) REVERT: E 123 ASP cc_start: 0.9162 (m-30) cc_final: 0.8936 (m-30) REVERT: E 129 ARG cc_start: 0.8565 (tpt90) cc_final: 0.8140 (tpt90) REVERT: F 85 ASP cc_start: 0.8754 (m-30) cc_final: 0.8480 (m-30) REVERT: H 85 LYS cc_start: 0.9361 (mttm) cc_final: 0.9024 (mmtt) REVERT: H 120 LYS cc_start: 0.9262 (tttm) cc_final: 0.9048 (tttp) REVERT: C 15 LYS cc_start: 0.7752 (ptpp) cc_final: 0.7536 (ptpp) REVERT: C 95 LYS cc_start: 0.9227 (tptm) cc_final: 0.8889 (ttmm) REVERT: G 64 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8740 (tm-30) outliers start: 9 outliers final: 7 residues processed: 160 average time/residue: 0.3157 time to fit residues: 68.3234 Evaluate side-chains 158 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 118 VAL 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 30.0000 chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 0.1980 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8669 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 13658 Z= 0.408 Angle : 0.637 8.574 19696 Z= 0.373 Chirality : 0.038 0.178 2240 Planarity : 0.004 0.033 1477 Dihedral : 30.036 150.315 4170 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.99 % Favored : 96.89 % Rotamer: Outliers : 2.08 % Allowed : 15.40 % Favored : 82.52 % 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: 2.59 (0.22), residues: 560 sheet: -0.08 (1.20), residues: 20 loop : -1.00 (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 0.037 0.002 TYR F 88 ARG 0.004 0.000 ARG D 86 *********************** 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 172 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 158 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8794 (pm20) cc_final: 0.8298 (pm20) REVERT: A 76 GLN cc_start: 0.8904 (tm-30) cc_final: 0.8622 (tm-30) REVERT: B 88 TYR cc_start: 0.8920 (m-10) cc_final: 0.8110 (m-80) REVERT: D 71 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8224 (tp30) REVERT: E 123 ASP cc_start: 0.9108 (m-30) cc_final: 0.8907 (m-30) REVERT: E 129 ARG cc_start: 0.8563 (tpt90) cc_final: 0.8087 (tpt90) REVERT: F 85 ASP cc_start: 0.8757 (m-30) cc_final: 0.8507 (m-30) REVERT: H 85 LYS cc_start: 0.9360 (mttm) cc_final: 0.9037 (mmtt) REVERT: H 120 LYS cc_start: 0.9202 (tttm) cc_final: 0.8959 (tttp) REVERT: C 95 LYS cc_start: 0.9231 (tptm) cc_final: 0.8815 (ttmm) REVERT: G 64 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8226 (tm-30) outliers start: 14 outliers final: 12 residues processed: 164 average time/residue: 0.3224 time to fit residues: 70.7748 Evaluate side-chains 165 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 153 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 73 GLU 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 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: 2.9990 chunk 94 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN E 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8617 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13658 Z= 0.205 Angle : 0.558 9.438 19696 Z= 0.331 Chirality : 0.034 0.186 2240 Planarity : 0.004 0.035 1477 Dihedral : 29.804 149.391 4170 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.15 % Favored : 97.73 % Rotamer: Outliers : 1.94 % Allowed : 16.50 % Favored : 81.55 % 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: 2.48 (0.30), residues: 839 helix: 2.80 (0.22), residues: 560 sheet: 0.04 (1.20), residues: 20 loop : -0.95 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.008 0.001 PHE A 67 TYR 0.020 0.002 TYR F 88 ARG 0.006 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 163 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 150 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8764 (pm20) cc_final: 0.8232 (pm20) REVERT: A 76 GLN cc_start: 0.8793 (tm-30) cc_final: 0.8509 (tm-30) REVERT: B 88 TYR cc_start: 0.8962 (m-10) cc_final: 0.8368 (m-10) REVERT: D 71 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8394 (tp30) REVERT: E 129 ARG cc_start: 0.8537 (tpt90) cc_final: 0.8113 (tpt90) REVERT: F 85 ASP cc_start: 0.8743 (m-30) cc_final: 0.8472 (m-30) REVERT: F 88 TYR cc_start: 0.7605 (m-10) cc_final: 0.7351 (m-10) REVERT: H 68 ASP cc_start: 0.9078 (t0) cc_final: 0.8877 (t0) REVERT: H 85 LYS cc_start: 0.9371 (mttm) cc_final: 0.9051 (mmtt) REVERT: H 93 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7606 (pt0) REVERT: H 120 LYS cc_start: 0.9249 (tttm) cc_final: 0.9024 (tttp) REVERT: C 15 LYS cc_start: 0.7790 (ptpp) cc_final: 0.7541 (pttm) REVERT: C 95 LYS cc_start: 0.9227 (tptm) cc_final: 0.8887 (ttmm) REVERT: G 64 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8530 (tm-30) outliers start: 13 outliers final: 7 residues processed: 158 average time/residue: 0.3186 time to fit residues: 67.3392 Evaluate side-chains 155 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 147 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 110 CYS 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 H residue 93 GLU 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: 2.9990 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8671 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 13658 Z= 0.416 Angle : 0.644 9.946 19696 Z= 0.375 Chirality : 0.038 0.181 2240 Planarity : 0.004 0.034 1477 Dihedral : 30.055 150.342 4170 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.99 % Favored : 96.77 % Rotamer: Outliers : 2.08 % Allowed : 17.20 % 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: 2.12 (0.30), residues: 839 helix: 2.55 (0.22), residues: 560 sheet: -0.35 (1.19), residues: 20 loop : -1.12 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.010 0.002 PHE B 61 TYR 0.027 0.002 TYR H 83 ARG 0.006 0.000 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 169 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 155 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8830 (pm20) cc_final: 0.8287 (pm20) REVERT: A 76 GLN cc_start: 0.8892 (tm-30) cc_final: 0.8586 (tm-30) REVERT: B 88 TYR cc_start: 0.8916 (m-10) cc_final: 0.8119 (m-80) REVERT: D 71 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8139 (tp30) REVERT: E 129 ARG cc_start: 0.8554 (tpt90) cc_final: 0.8079 (tpt90) REVERT: F 85 ASP cc_start: 0.8788 (m-30) cc_final: 0.8527 (m-30) REVERT: F 88 TYR cc_start: 0.7904 (m-10) cc_final: 0.7662 (m-10) REVERT: H 85 LYS cc_start: 0.9380 (mttm) cc_final: 0.9049 (mmtt) REVERT: H 93 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7771 (pt0) REVERT: H 120 LYS cc_start: 0.9191 (tttm) cc_final: 0.8947 (tttp) REVERT: C 15 LYS cc_start: 0.7739 (ptpp) cc_final: 0.7493 (pttm) REVERT: C 95 LYS cc_start: 0.9220 (tptm) cc_final: 0.8834 (ttmm) REVERT: G 64 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8383 (tm-30) outliers start: 14 outliers final: 12 residues processed: 162 average time/residue: 0.3095 time to fit residues: 67.2709 Evaluate side-chains 166 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 153 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 110 CYS 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 93 GLU Chi-restraints excluded: chain H residue 111 VAL 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: 0.5980 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 10.0000 chunk 94 optimal weight: 0.3980 chunk 99 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8605 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13658 Z= 0.190 Angle : 0.562 10.509 19696 Z= 0.332 Chirality : 0.033 0.189 2240 Planarity : 0.004 0.036 1477 Dihedral : 29.783 149.094 4170 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.91 % Favored : 97.85 % Rotamer: Outliers : 1.66 % Allowed : 17.34 % Favored : 81.00 % 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: 2.46 (0.30), residues: 839 helix: 2.81 (0.22), residues: 559 sheet: 0.02 (1.23), residues: 20 loop : -1.00 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 75 PHE 0.007 0.001 PHE A 78 TYR 0.021 0.001 TYR C 39 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 165 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 154 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8781 (pm20) cc_final: 0.8218 (pm20) REVERT: A 76 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8510 (tm-30) REVERT: B 88 TYR cc_start: 0.8942 (m-10) cc_final: 0.8351 (m-10) REVERT: D 71 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8367 (tp30) REVERT: E 129 ARG cc_start: 0.8555 (tpt90) cc_final: 0.8149 (tpt90) REVERT: F 85 ASP cc_start: 0.8747 (m-30) cc_final: 0.8490 (m-30) REVERT: H 85 LYS cc_start: 0.9362 (mttm) cc_final: 0.9031 (mmtt) REVERT: H 93 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7683 (pt0) REVERT: H 120 LYS cc_start: 0.9246 (tttm) cc_final: 0.9023 (tttp) REVERT: C 95 LYS cc_start: 0.9203 (tptm) cc_final: 0.8844 (ttmm) REVERT: G 64 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8530 (tm-30) outliers start: 11 outliers final: 10 residues processed: 162 average time/residue: 0.3114 time to fit residues: 67.7334 Evaluate side-chains 155 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 110 CYS 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 93 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 0.0980 chunk 99 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 0.2980 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8602 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13658 Z= 0.195 Angle : 0.563 11.379 19696 Z= 0.332 Chirality : 0.033 0.186 2240 Planarity : 0.004 0.036 1477 Dihedral : 29.768 149.338 4170 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.27 % Favored : 97.49 % Rotamer: Outliers : 1.66 % Allowed : 17.61 % 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: 2.48 (0.30), residues: 839 helix: 2.82 (0.22), residues: 559 sheet: 0.08 (1.24), residues: 20 loop : -0.98 (0.36), residues: 260 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 0.028 0.002 TYR F 88 ARG 0.007 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 159 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 148 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8785 (pm20) cc_final: 0.8214 (pm20) REVERT: A 73 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7342 (mt-10) REVERT: A 76 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8519 (tm-30) REVERT: B 88 TYR cc_start: 0.8929 (m-10) cc_final: 0.8366 (m-10) REVERT: D 71 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8364 (tp30) REVERT: E 129 ARG cc_start: 0.8554 (tpt90) cc_final: 0.8144 (tpt90) REVERT: F 85 ASP cc_start: 0.8757 (m-30) cc_final: 0.8486 (m-30) REVERT: H 85 LYS cc_start: 0.9360 (mttm) cc_final: 0.9027 (mmtt) REVERT: H 93 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7628 (pt0) REVERT: H 120 LYS cc_start: 0.9247 (tttm) cc_final: 0.9022 (tttp) REVERT: C 95 LYS cc_start: 0.9197 (tptm) cc_final: 0.8836 (ttmm) REVERT: G 64 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8526 (tm-30) outliers start: 11 outliers final: 10 residues processed: 156 average time/residue: 0.3121 time to fit residues: 65.6430 Evaluate side-chains 154 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 143 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 110 CYS 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 93 GLU 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: 2.9990 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8658 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 13658 Z= 0.379 Angle : 0.634 11.711 19696 Z= 0.369 Chirality : 0.038 0.182 2240 Planarity : 0.004 0.035 1477 Dihedral : 29.992 150.480 4170 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.39 % Favored : 97.37 % Rotamer: Outliers : 1.66 % Allowed : 17.89 % Favored : 80.44 % 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: 2.24 (0.30), residues: 839 helix: 2.63 (0.22), residues: 560 sheet: -0.29 (1.21), residues: 20 loop : -1.04 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 49 PHE 0.009 0.002 PHE B 61 TYR 0.056 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 159 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 148 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8840 (pm20) cc_final: 0.8275 (pm20) REVERT: A 76 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8605 (tm-30) REVERT: B 88 TYR cc_start: 0.8881 (m-10) cc_final: 0.8200 (m-10) REVERT: D 71 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8141 (tp30) REVERT: E 129 ARG cc_start: 0.8551 (tpt90) cc_final: 0.8071 (tpt90) REVERT: F 85 ASP cc_start: 0.8756 (m-30) cc_final: 0.8504 (m-30) REVERT: H 85 LYS cc_start: 0.9356 (mttm) cc_final: 0.9035 (mmtt) REVERT: H 93 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7788 (pt0) REVERT: H 120 LYS cc_start: 0.9194 (tttm) cc_final: 0.8947 (tttp) REVERT: C 95 LYS cc_start: 0.9218 (tptm) cc_final: 0.8841 (ttmm) REVERT: G 64 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8380 (tm-30) outliers start: 11 outliers final: 10 residues processed: 153 average time/residue: 0.3154 time to fit residues: 64.9148 Evaluate side-chains 158 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 147 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 110 CYS 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 93 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 12 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.101784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.065881 restraints weight = 40229.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.068283 restraints weight = 18758.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.069972 restraints weight = 12465.620| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13658 Z= 0.273 Angle : 0.591 11.174 19696 Z= 0.346 Chirality : 0.035 0.176 2240 Planarity : 0.004 0.035 1477 Dihedral : 29.857 149.526 4170 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.39 % Favored : 97.37 % Rotamer: Outliers : 1.80 % Allowed : 17.75 % Favored : 80.44 % 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: 2.33 (0.30), residues: 839 helix: 2.70 (0.22), residues: 559 sheet: -0.14 (1.23), residues: 20 loop : -1.02 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE A 67 TYR 0.037 0.002 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: 2252.57 seconds wall clock time: 40 minutes 44.41 seconds (2444.41 seconds total)