Starting phenix.real_space_refine on Fri Mar 15 14:52:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6se0_10151/03_2024/6se0_10151.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6se0_10151/03_2024/6se0_10151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6se0_10151/03_2024/6se0_10151.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6se0_10151/03_2024/6se0_10151.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6se0_10151/03_2024/6se0_10151.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6se0_10151/03_2024/6se0_10151.pdb" } resolution = 3.8 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= 0.003 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 288 5.49 5 S 10 5.16 5 C 6657 2.51 5 N 2256 2.21 5 O 2791 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 44": "NH1" <-> "NH2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D ARG 31": "NH1" <-> "NH2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 43": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E GLU 136": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H ARG 31": "NH1" <-> "NH2" Residue "H ARG 79": "NH1" <-> "NH2" Residue "H TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 93": "OE1" <-> "OE2" Residue "H GLU 105": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12002 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "B" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 845 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 6.61, per 1000 atoms: 0.55 Number of scatterers: 12002 At special positions: 0 Unit cell: (75.26, 119.78, 115.54, 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 10 16.00 P 288 15.00 O 2791 8.00 N 2256 7.00 C 6657 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: 6.49 Conformation dependent library (CDL) restraints added in 1.1 seconds 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1414 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 9 sheets defined 70.8% alpha, 2.6% beta 145 base pairs and 257 stacking pairs defined. Time for finding SS restraints: 5.64 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 removed outlier: 3.806A pdb=" N GLU A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.824A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.509A pdb=" N ALA A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.783A pdb=" N LEU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.593A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.202A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.583A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.616A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 removed outlier: 3.700A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.664A pdb=" N VAL D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.547A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.520A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 122 removed outlier: 3.522A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.838A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 116 removed outlier: 3.602A pdb=" N LEU E 91 " --> pdb=" O GLN E 87 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 134 removed outlier: 3.804A pdb=" N GLY E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.542A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.289A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.509A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 38 removed outlier: 3.799A pdb=" N ASN G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.550A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.582A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.577A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.591A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 7.240A pdb=" N ASN A 85 " --> 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 120 through 121 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.870A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'E' and resid 85 through 86 removed outlier: 7.015A pdb=" N ASN E 85 " --> 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 120 through 121 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.527A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 377 hydrogen bonds defined for protein. 1119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 728 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 257 stacking parallelities Total time for adding SS restraints: 4.50 Time building geometry restraints manager: 6.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2004 1.33 - 1.45: 4338 1.45 - 1.57: 5874 1.57 - 1.68: 576 1.68 - 1.80: 18 Bond restraints: 12810 Sorted by residual: bond pdb=" C3' DA J 6 " pdb=" O3' DA J 6 " ideal model delta sigma weight residual 1.422 1.358 0.064 3.00e-02 1.11e+03 4.55e+00 bond pdb=" SD MET G 51 " pdb=" CE MET G 51 " ideal model delta sigma weight residual 1.791 1.738 0.053 2.50e-02 1.60e+03 4.46e+00 bond pdb=" CG1 ILE A 132 " pdb=" CD1 ILE A 132 " ideal model delta sigma weight residual 1.513 1.441 0.072 3.90e-02 6.57e+02 3.41e+00 bond pdb=" CB ILE A 51 " pdb=" CG2 ILE A 51 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.23e+00 bond pdb=" CB TRP E 86 " pdb=" CG TRP E 86 " ideal model delta sigma weight residual 1.498 1.444 0.054 3.10e-02 1.04e+03 3.07e+00 ... (remaining 12805 not shown) Histogram of bond angle deviations from ideal: 98.12 - 105.30: 1325 105.30 - 112.48: 7020 112.48 - 119.67: 4427 119.67 - 126.85: 4976 126.85 - 134.03: 787 Bond angle restraints: 18535 Sorted by residual: angle pdb=" CA LEU F 90 " pdb=" CB LEU F 90 " pdb=" CG LEU F 90 " ideal model delta sigma weight residual 116.30 98.69 17.61 3.50e+00 8.16e-02 2.53e+01 angle pdb=" CB MET G 51 " pdb=" CG MET G 51 " pdb=" SD MET G 51 " ideal model delta sigma weight residual 112.70 126.00 -13.30 3.00e+00 1.11e-01 1.97e+01 angle pdb=" C ILE G 87 " pdb=" N ARG G 88 " pdb=" CA ARG G 88 " ideal model delta sigma weight residual 121.94 114.53 7.41 2.00e+00 2.50e-01 1.37e+01 angle pdb=" CA VAL C 107 " pdb=" CB VAL C 107 " pdb=" CG1 VAL C 107 " ideal model delta sigma weight residual 110.40 116.30 -5.90 1.70e+00 3.46e-01 1.21e+01 angle pdb=" CA ARG E 43 " pdb=" CB ARG E 43 " pdb=" CG ARG E 43 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 ... (remaining 18530 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.26: 5109 29.26 - 58.52: 1726 58.52 - 87.78: 87 87.78 - 117.04: 3 117.04 - 146.30: 1 Dihedral angle restraints: 6926 sinusoidal: 4729 harmonic: 2197 Sorted by residual: dihedral pdb=" CA ILE B 29 " pdb=" C ILE B 29 " pdb=" N THR B 30 " pdb=" CA THR B 30 " ideal model delta harmonic sigma weight residual 180.00 -160.46 -19.54 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 73.70 146.30 1 3.50e+01 8.16e-04 1.44e+01 dihedral pdb=" CA GLN G 112 " pdb=" C GLN G 112 " pdb=" N ALA G 113 " pdb=" CA ALA G 113 " ideal model delta harmonic sigma weight residual -180.00 -163.04 -16.96 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 6923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1514 0.058 - 0.116: 486 0.116 - 0.175: 86 0.175 - 0.233: 9 0.233 - 0.291: 4 Chirality restraints: 2099 Sorted by residual: chirality pdb=" CG LEU G 108 " pdb=" CB LEU G 108 " pdb=" CD1 LEU G 108 " pdb=" CD2 LEU G 108 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" P DG J 50 " pdb=" OP1 DG J 50 " pdb=" OP2 DG J 50 " pdb=" O5' DG J 50 " both_signs ideal model delta sigma weight residual True 2.35 -2.60 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB ILE D 54 " pdb=" CA ILE D 54 " pdb=" CG1 ILE D 54 " pdb=" CG2 ILE D 54 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 2096 not shown) Planarity restraints: 1338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.063 5.00e-02 4.00e+02 9.47e-02 1.44e+01 pdb=" N PRO G 80 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.058 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO C 80 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 119 " 0.017 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C VAL A 119 " -0.057 2.00e-02 2.50e+03 pdb=" O VAL A 119 " 0.020 2.00e-02 2.50e+03 pdb=" N THR A 120 " 0.019 2.00e-02 2.50e+03 ... (remaining 1335 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2322 2.78 - 3.31: 10081 3.31 - 3.84: 23976 3.84 - 4.37: 26839 4.37 - 4.90: 37586 Nonbonded interactions: 100804 Sorted by model distance: nonbonded pdb=" OG SER G 18 " pdb=" O LEU G 23 " model vdw 2.248 2.440 nonbonded pdb=" O2 DC I -56 " pdb=" N2 DG J 56 " model vdw 2.286 2.496 nonbonded pdb=" O2 DC I -62 " pdb=" N2 DG J 62 " model vdw 2.299 2.496 nonbonded pdb=" OH TYR H 40 " pdb=" OP1 DG I 48 " model vdw 2.319 2.440 nonbonded pdb=" OG1 THR E 113 " pdb=" O THR E 120 " model vdw 2.343 2.440 ... (remaining 100799 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' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 10 through 116) selection = (chain 'G' and resid 10 through 116) } ncs_group { reference = (chain 'D' and resid 31 through 124) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 3.680 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 38.400 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 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:2.900 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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 : 0.009 0.074 12810 Z= 0.486 Angle : 1.012 17.610 18535 Z= 0.574 Chirality : 0.057 0.291 2099 Planarity : 0.008 0.095 1338 Dihedral : 28.079 146.298 5512 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % 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: -2.82 (0.23), residues: 749 helix: -1.67 (0.17), residues: 511 sheet: None (None), residues: 0 loop : -1.94 (0.31), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 86 HIS 0.015 0.003 HIS F 75 PHE 0.025 0.004 PHE A 78 TYR 0.035 0.004 TYR A 110 ARG 0.011 0.001 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9426 (tp30) cc_final: 0.9176 (tp30) REVERT: A 85 ASN cc_start: 0.8494 (m-40) cc_final: 0.8198 (m-40) REVERT: B 45 ARG cc_start: 0.7613 (mtm180) cc_final: 0.6389 (ttm110) REVERT: B 79 LYS cc_start: 0.8156 (mtpt) cc_final: 0.7575 (mtmm) REVERT: C 56 GLU cc_start: 0.6795 (tt0) cc_final: 0.6576 (tt0) REVERT: C 57 TYR cc_start: 0.9003 (t80) cc_final: 0.8528 (t80) REVERT: C 61 GLU cc_start: 0.8731 (tp30) cc_final: 0.8261 (tp30) REVERT: C 92 GLU cc_start: 0.8295 (tt0) cc_final: 0.7903 (tt0) REVERT: C 95 LYS cc_start: 0.8448 (ttmt) cc_final: 0.7929 (tppt) REVERT: D 113 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7848 (mt-10) REVERT: D 116 LYS cc_start: 0.8782 (ttpp) cc_final: 0.8555 (ttmm) REVERT: E 49 LYS cc_start: 0.8950 (ptmt) cc_final: 0.8452 (ptmt) REVERT: E 64 LYS cc_start: 0.7947 (mtpt) cc_final: 0.7371 (tptt) REVERT: E 73 GLU cc_start: 0.9093 (tp30) cc_final: 0.8453 (tp30) REVERT: G 71 ARG cc_start: 0.8700 (mmm-85) cc_final: 0.7999 (mtm180) REVERT: G 92 GLU cc_start: 0.8177 (tt0) cc_final: 0.7792 (tt0) REVERT: H 93 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8066 (mm-30) REVERT: H 95 GLN cc_start: 0.8108 (tt0) cc_final: 0.7145 (tm-30) REVERT: H 105 GLU cc_start: 0.8171 (tp30) cc_final: 0.7551 (tp30) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.3498 time to fit residues: 116.3767 Evaluate side-chains 185 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 104 HIS B 64 ASN D 95 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN G 31 HIS G 73 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12810 Z= 0.206 Angle : 0.635 10.458 18535 Z= 0.369 Chirality : 0.035 0.144 2099 Planarity : 0.005 0.066 1338 Dihedral : 30.164 147.758 4015 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 4.63 % Allowed : 19.62 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.27), residues: 749 helix: 0.35 (0.20), residues: 542 sheet: None (None), residues: 0 loop : -1.63 (0.34), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 47 HIS 0.005 0.001 HIS F 75 PHE 0.007 0.001 PHE A 106 TYR 0.019 0.002 TYR H 83 ARG 0.005 0.001 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 209 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9378 (tp30) cc_final: 0.9151 (tp30) REVERT: A 85 ASN cc_start: 0.8502 (m-40) cc_final: 0.8161 (m-40) REVERT: A 95 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7537 (tp40) REVERT: A 110 TYR cc_start: 0.7550 (t80) cc_final: 0.7323 (t80) REVERT: B 44 LYS cc_start: 0.8412 (tttt) cc_final: 0.7792 (mmmt) REVERT: B 45 ARG cc_start: 0.7344 (mtm180) cc_final: 0.6775 (mtt90) REVERT: B 84 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7355 (mtm) REVERT: C 56 GLU cc_start: 0.6651 (tt0) cc_final: 0.6372 (tt0) REVERT: C 61 GLU cc_start: 0.8694 (tp30) cc_final: 0.8240 (tp30) REVERT: D 76 GLU cc_start: 0.8418 (tp30) cc_final: 0.8140 (tp30) REVERT: E 49 LYS cc_start: 0.9028 (ptmt) cc_final: 0.8447 (ptmt) REVERT: E 64 LYS cc_start: 0.7865 (mtpt) cc_final: 0.7353 (tptt) REVERT: E 73 GLU cc_start: 0.9054 (tp30) cc_final: 0.8351 (tm-30) REVERT: G 71 ARG cc_start: 0.8748 (mmm-85) cc_final: 0.7849 (mtm-85) REVERT: G 92 GLU cc_start: 0.8261 (tt0) cc_final: 0.7941 (tt0) REVERT: H 93 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7995 (mm-30) REVERT: H 95 GLN cc_start: 0.7994 (tt0) cc_final: 0.7023 (tm-30) REVERT: H 105 GLU cc_start: 0.7994 (tp30) cc_final: 0.7488 (tp30) outliers start: 29 outliers final: 14 residues processed: 220 average time/residue: 0.2744 time to fit residues: 81.8376 Evaluate side-chains 192 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 176 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 111 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 73 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN G 68 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 12810 Z= 0.330 Angle : 0.708 13.162 18535 Z= 0.405 Chirality : 0.038 0.151 2099 Planarity : 0.005 0.047 1338 Dihedral : 30.268 147.820 4015 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 6.70 % Allowed : 22.81 % Favored : 70.49 % 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: -0.01 (0.29), residues: 749 helix: 0.63 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -1.58 (0.35), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 47 HIS 0.007 0.002 HIS F 75 PHE 0.013 0.002 PHE A 84 TYR 0.023 0.003 TYR C 57 ARG 0.004 0.001 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 172 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 77 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8152 (ttpp) REVERT: A 85 ASN cc_start: 0.8585 (m-40) cc_final: 0.8267 (m110) REVERT: A 95 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7620 (tp40) REVERT: B 44 LYS cc_start: 0.8403 (tttt) cc_final: 0.7966 (mmmt) REVERT: B 45 ARG cc_start: 0.7479 (mtm180) cc_final: 0.6801 (mtt90) REVERT: B 51 TYR cc_start: 0.8118 (m-80) cc_final: 0.7712 (m-80) REVERT: B 84 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7194 (mtm) REVERT: C 57 TYR cc_start: 0.8744 (t80) cc_final: 0.8109 (t80) REVERT: D 76 GLU cc_start: 0.8356 (tp30) cc_final: 0.8145 (tp30) REVERT: D 79 ARG cc_start: 0.8106 (ptp90) cc_final: 0.7037 (ptp90) REVERT: D 86 ARG cc_start: 0.8341 (mmp80) cc_final: 0.8074 (mmp80) REVERT: E 49 LYS cc_start: 0.9137 (ptmt) cc_final: 0.8625 (ptmt) REVERT: E 64 LYS cc_start: 0.8029 (mtpt) cc_final: 0.7541 (tptt) REVERT: E 73 GLU cc_start: 0.9137 (tp30) cc_final: 0.8418 (tm-30) REVERT: E 99 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7589 (tp30) REVERT: E 110 TYR cc_start: 0.7069 (t80) cc_final: 0.6798 (t80) REVERT: F 50 ILE cc_start: 0.8775 (tp) cc_final: 0.8128 (mm) REVERT: F 53 GLU cc_start: 0.8197 (tt0) cc_final: 0.7790 (tt0) REVERT: G 71 ARG cc_start: 0.8793 (mmm-85) cc_final: 0.7935 (mtm-85) REVERT: H 93 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8016 (mm-30) REVERT: H 95 GLN cc_start: 0.8229 (tt0) cc_final: 0.7139 (tm-30) outliers start: 42 outliers final: 26 residues processed: 192 average time/residue: 0.2572 time to fit residues: 67.6944 Evaluate side-chains 190 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 161 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 111 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 87 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12810 Z= 0.175 Angle : 0.604 8.981 18535 Z= 0.350 Chirality : 0.034 0.141 2099 Planarity : 0.004 0.042 1338 Dihedral : 29.984 146.431 4015 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 4.78 % Allowed : 25.68 % Favored : 69.54 % 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: 0.57 (0.30), residues: 749 helix: 1.09 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.47 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 47 HIS 0.005 0.001 HIS F 75 PHE 0.008 0.001 PHE H 65 TYR 0.028 0.002 TYR H 83 ARG 0.004 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 193 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8525 (m-40) cc_final: 0.7758 (t0) REVERT: A 110 TYR cc_start: 0.7480 (t80) cc_final: 0.7227 (t80) REVERT: B 24 ASP cc_start: 0.7900 (t0) cc_final: 0.7353 (p0) REVERT: B 44 LYS cc_start: 0.8464 (tttt) cc_final: 0.7838 (mmmt) REVERT: B 45 ARG cc_start: 0.7279 (mtm180) cc_final: 0.6866 (mtt90) REVERT: B 51 TYR cc_start: 0.7921 (m-80) cc_final: 0.7463 (m-80) REVERT: B 84 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7209 (mtm) REVERT: C 64 GLU cc_start: 0.8470 (tp30) cc_final: 0.7937 (mm-30) REVERT: C 92 GLU cc_start: 0.8084 (tt0) cc_final: 0.7179 (tt0) REVERT: D 85 LYS cc_start: 0.8964 (tppt) cc_final: 0.8756 (tppt) REVERT: D 86 ARG cc_start: 0.8454 (mmp80) cc_final: 0.8051 (mmp80) REVERT: D 105 GLU cc_start: 0.8936 (pm20) cc_final: 0.8690 (pm20) REVERT: D 106 LEU cc_start: 0.9518 (tp) cc_final: 0.9289 (mt) REVERT: D 120 LYS cc_start: 0.8743 (ttmm) cc_final: 0.8275 (tttm) REVERT: E 49 LYS cc_start: 0.9056 (ptmt) cc_final: 0.8515 (ptmt) REVERT: E 73 GLU cc_start: 0.9093 (tp30) cc_final: 0.8388 (tm-30) REVERT: E 99 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7810 (mm-30) REVERT: E 110 TYR cc_start: 0.6781 (t80) cc_final: 0.6561 (t80) REVERT: F 31 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7554 (tttt) REVERT: F 53 GLU cc_start: 0.8169 (tt0) cc_final: 0.7710 (tt0) REVERT: G 71 ARG cc_start: 0.8726 (mmm-85) cc_final: 0.7838 (ptp-170) REVERT: H 62 MET cc_start: 0.8966 (mmm) cc_final: 0.8725 (mmm) REVERT: H 93 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7907 (mm-30) REVERT: H 95 GLN cc_start: 0.8092 (tt0) cc_final: 0.7063 (tm-30) outliers start: 30 outliers final: 18 residues processed: 206 average time/residue: 0.2569 time to fit residues: 73.1093 Evaluate side-chains 193 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 173 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 111 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 87 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12810 Z= 0.217 Angle : 0.614 10.709 18535 Z= 0.355 Chirality : 0.034 0.177 2099 Planarity : 0.004 0.039 1338 Dihedral : 30.034 145.984 4015 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.78 % Allowed : 26.48 % Favored : 68.74 % 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: 0.62 (0.30), residues: 749 helix: 1.18 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -1.61 (0.35), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 47 HIS 0.006 0.001 HIS F 75 PHE 0.011 0.001 PHE A 67 TYR 0.028 0.002 TYR H 83 ARG 0.003 0.000 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8539 (m-40) cc_final: 0.7719 (t0) REVERT: A 110 TYR cc_start: 0.7708 (t80) cc_final: 0.7391 (t80) REVERT: B 24 ASP cc_start: 0.7951 (t0) cc_final: 0.7397 (p0) REVERT: B 45 ARG cc_start: 0.7295 (mtm180) cc_final: 0.6257 (ttm170) REVERT: B 51 TYR cc_start: 0.8021 (m-80) cc_final: 0.7598 (m-80) REVERT: B 84 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7086 (mtp) REVERT: C 64 GLU cc_start: 0.8485 (tp30) cc_final: 0.7955 (mm-30) REVERT: C 82 HIS cc_start: 0.8275 (m-70) cc_final: 0.8023 (m-70) REVERT: C 92 GLU cc_start: 0.8151 (tt0) cc_final: 0.7179 (tt0) REVERT: D 59 MET cc_start: 0.7990 (tpp) cc_final: 0.7598 (tpp) REVERT: D 86 ARG cc_start: 0.8408 (mmp80) cc_final: 0.8000 (mmp80) REVERT: D 105 GLU cc_start: 0.8987 (pm20) cc_final: 0.8735 (pm20) REVERT: D 106 LEU cc_start: 0.9511 (tp) cc_final: 0.9221 (mt) REVERT: D 120 LYS cc_start: 0.8864 (ttmm) cc_final: 0.8421 (tttm) REVERT: E 49 LYS cc_start: 0.9080 (ptmt) cc_final: 0.8526 (ptmt) REVERT: E 73 GLU cc_start: 0.9137 (tp30) cc_final: 0.8369 (tp30) REVERT: E 99 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7638 (mm-30) REVERT: E 110 TYR cc_start: 0.6901 (t80) cc_final: 0.6585 (t80) REVERT: F 31 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7599 (tttm) REVERT: F 53 GLU cc_start: 0.8140 (tt0) cc_final: 0.7630 (tt0) REVERT: G 71 ARG cc_start: 0.8759 (mmm-85) cc_final: 0.7923 (ptp-170) REVERT: H 62 MET cc_start: 0.8997 (mmm) cc_final: 0.8764 (mmm) REVERT: H 93 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7906 (mm-30) REVERT: H 95 GLN cc_start: 0.8075 (tt0) cc_final: 0.7170 (tm-30) outliers start: 30 outliers final: 21 residues processed: 197 average time/residue: 0.2589 time to fit residues: 70.3312 Evaluate side-chains 194 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 171 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 111 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12810 Z= 0.254 Angle : 0.636 11.369 18535 Z= 0.366 Chirality : 0.035 0.155 2099 Planarity : 0.004 0.036 1338 Dihedral : 30.187 145.939 4015 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 5.58 % Allowed : 27.11 % Favored : 67.30 % 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: 0.56 (0.30), residues: 749 helix: 1.11 (0.23), residues: 547 sheet: None (None), residues: 0 loop : -1.62 (0.36), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 47 HIS 0.006 0.001 HIS F 75 PHE 0.011 0.001 PHE A 84 TYR 0.056 0.003 TYR H 83 ARG 0.004 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 173 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8608 (m-40) cc_final: 0.7711 (t0) REVERT: A 110 TYR cc_start: 0.7667 (t80) cc_final: 0.7296 (t80) REVERT: B 24 ASP cc_start: 0.8053 (t0) cc_final: 0.7497 (p0) REVERT: B 45 ARG cc_start: 0.7311 (mtm180) cc_final: 0.6267 (ttm170) REVERT: B 51 TYR cc_start: 0.8087 (m-80) cc_final: 0.7681 (m-80) REVERT: B 84 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7148 (mtm) REVERT: C 64 GLU cc_start: 0.8443 (tp30) cc_final: 0.8014 (mm-30) REVERT: D 59 MET cc_start: 0.8026 (tpp) cc_final: 0.7644 (tpp) REVERT: E 49 LYS cc_start: 0.9069 (ptmt) cc_final: 0.8548 (ptmt) REVERT: E 73 GLU cc_start: 0.9145 (tp30) cc_final: 0.8333 (tm-30) REVERT: E 110 TYR cc_start: 0.7022 (t80) cc_final: 0.6664 (t80) REVERT: F 31 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7513 (tttm) REVERT: F 53 GLU cc_start: 0.8126 (tt0) cc_final: 0.7670 (tt0) REVERT: F 88 TYR cc_start: 0.7948 (m-80) cc_final: 0.7669 (m-80) REVERT: G 71 ARG cc_start: 0.8786 (mmm-85) cc_final: 0.7946 (ptp-170) REVERT: H 93 GLU cc_start: 0.8461 (mm-30) cc_final: 0.7975 (mm-30) REVERT: H 95 GLN cc_start: 0.8165 (tt0) cc_final: 0.7273 (tm-30) outliers start: 35 outliers final: 28 residues processed: 189 average time/residue: 0.2365 time to fit residues: 63.1582 Evaluate side-chains 194 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 164 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 111 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12810 Z= 0.210 Angle : 0.614 10.127 18535 Z= 0.353 Chirality : 0.034 0.158 2099 Planarity : 0.004 0.035 1338 Dihedral : 30.137 145.221 4015 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.94 % Allowed : 29.35 % Favored : 65.71 % 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: 0.78 (0.30), residues: 749 helix: 1.31 (0.23), residues: 533 sheet: None (None), residues: 0 loop : -1.47 (0.35), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 47 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.001 PHE E 84 TYR 0.040 0.002 TYR H 83 ARG 0.003 0.000 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 175 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8615 (m-40) cc_final: 0.7781 (t0) REVERT: A 110 TYR cc_start: 0.7677 (t80) cc_final: 0.7394 (t80) REVERT: B 24 ASP cc_start: 0.7988 (t0) cc_final: 0.7382 (p0) REVERT: B 45 ARG cc_start: 0.7486 (mtm180) cc_final: 0.6779 (mtt90) REVERT: B 51 TYR cc_start: 0.8043 (m-80) cc_final: 0.7645 (m-80) REVERT: B 84 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7129 (mtm) REVERT: C 64 GLU cc_start: 0.8406 (tp30) cc_final: 0.8006 (mm-30) REVERT: C 92 GLU cc_start: 0.8091 (tt0) cc_final: 0.7390 (tt0) REVERT: D 59 MET cc_start: 0.8010 (tpp) cc_final: 0.7626 (tpp) REVERT: D 106 LEU cc_start: 0.9470 (tp) cc_final: 0.9252 (mt) REVERT: D 120 LYS cc_start: 0.8902 (ttmm) cc_final: 0.8439 (tttm) REVERT: E 49 LYS cc_start: 0.9046 (ptmt) cc_final: 0.8520 (ptmt) REVERT: E 73 GLU cc_start: 0.9114 (tp30) cc_final: 0.8292 (tm-30) REVERT: E 99 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7450 (mm-30) REVERT: E 110 TYR cc_start: 0.6997 (t80) cc_final: 0.6657 (t80) REVERT: F 31 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7475 (tttm) REVERT: F 53 GLU cc_start: 0.8116 (tt0) cc_final: 0.7668 (tt0) REVERT: G 71 ARG cc_start: 0.8768 (mmm-85) cc_final: 0.7917 (ptp-170) REVERT: H 93 GLU cc_start: 0.8477 (mm-30) cc_final: 0.7903 (mm-30) REVERT: H 95 GLN cc_start: 0.8110 (tt0) cc_final: 0.7221 (tm-30) outliers start: 31 outliers final: 27 residues processed: 188 average time/residue: 0.2485 time to fit residues: 65.7672 Evaluate side-chains 198 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 169 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 HIS ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12810 Z= 0.194 Angle : 0.614 8.423 18535 Z= 0.350 Chirality : 0.034 0.172 2099 Planarity : 0.004 0.037 1338 Dihedral : 30.061 144.820 4015 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 5.10 % Allowed : 29.35 % Favored : 65.55 % 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: 0.86 (0.30), residues: 749 helix: 1.35 (0.23), residues: 533 sheet: None (None), residues: 0 loop : -1.38 (0.35), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 47 HIS 0.005 0.001 HIS B 75 PHE 0.009 0.001 PHE H 65 TYR 0.057 0.002 TYR H 83 ARG 0.004 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 180 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8596 (m-40) cc_final: 0.8280 (m110) REVERT: A 110 TYR cc_start: 0.7456 (t80) cc_final: 0.7215 (t80) REVERT: B 24 ASP cc_start: 0.7890 (t0) cc_final: 0.7256 (p0) REVERT: B 45 ARG cc_start: 0.7233 (mtm180) cc_final: 0.6786 (mtt90) REVERT: B 51 TYR cc_start: 0.7985 (m-80) cc_final: 0.7573 (m-80) REVERT: B 79 LYS cc_start: 0.8367 (mtpp) cc_final: 0.7761 (mtmm) REVERT: B 84 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7136 (mtm) REVERT: C 64 GLU cc_start: 0.8354 (tp30) cc_final: 0.7990 (mm-30) REVERT: C 89 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.8361 (m110) REVERT: C 92 GLU cc_start: 0.8093 (tt0) cc_final: 0.7649 (tt0) REVERT: D 59 MET cc_start: 0.7982 (tpp) cc_final: 0.7565 (tpp) REVERT: E 49 LYS cc_start: 0.9029 (ptmt) cc_final: 0.8469 (ptmt) REVERT: E 73 GLU cc_start: 0.9117 (tp30) cc_final: 0.8259 (tm-30) REVERT: E 110 TYR cc_start: 0.6922 (t80) cc_final: 0.6577 (t80) REVERT: F 31 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7461 (tttm) REVERT: F 53 GLU cc_start: 0.8134 (tt0) cc_final: 0.7723 (tt0) REVERT: G 71 ARG cc_start: 0.8747 (mmm-85) cc_final: 0.7824 (ptp-110) REVERT: G 95 LYS cc_start: 0.8628 (ttmt) cc_final: 0.8426 (ttmm) REVERT: H 93 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7939 (mm-30) REVERT: H 95 GLN cc_start: 0.8091 (tt0) cc_final: 0.7175 (tm-30) outliers start: 32 outliers final: 25 residues processed: 194 average time/residue: 0.2589 time to fit residues: 69.9829 Evaluate side-chains 197 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 169 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 102 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12810 Z= 0.330 Angle : 0.705 14.013 18535 Z= 0.400 Chirality : 0.037 0.152 2099 Planarity : 0.005 0.037 1338 Dihedral : 30.467 146.231 4015 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 6.70 % Allowed : 28.39 % Favored : 64.91 % 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: 0.32 (0.29), residues: 749 helix: 0.98 (0.23), residues: 523 sheet: None (None), residues: 0 loop : -1.54 (0.33), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 47 HIS 0.007 0.002 HIS F 75 PHE 0.021 0.002 PHE A 67 TYR 0.078 0.004 TYR H 83 ARG 0.004 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 166 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8611 (m-40) cc_final: 0.8269 (m110) REVERT: A 128 LEU cc_start: 0.8555 (tt) cc_final: 0.8298 (tp) REVERT: B 44 LYS cc_start: 0.8466 (tttt) cc_final: 0.8261 (pttt) REVERT: B 45 ARG cc_start: 0.7496 (mtm180) cc_final: 0.6632 (ttm170) REVERT: B 51 TYR cc_start: 0.8141 (m-80) cc_final: 0.7792 (m-80) REVERT: B 84 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7156 (mtm) REVERT: C 64 GLU cc_start: 0.8505 (tp30) cc_final: 0.8105 (mm-30) REVERT: D 59 MET cc_start: 0.8114 (tpp) cc_final: 0.7729 (tpp) REVERT: E 49 LYS cc_start: 0.9024 (ptmt) cc_final: 0.8466 (ptmt) REVERT: E 73 GLU cc_start: 0.9159 (tp30) cc_final: 0.8332 (tm-30) REVERT: E 110 TYR cc_start: 0.7092 (t80) cc_final: 0.6699 (t80) REVERT: F 31 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7507 (tttm) REVERT: F 50 ILE cc_start: 0.8876 (tp) cc_final: 0.8230 (mm) REVERT: F 53 GLU cc_start: 0.8156 (tt0) cc_final: 0.7736 (tt0) REVERT: G 71 ARG cc_start: 0.8777 (mmm-85) cc_final: 0.7876 (ptp-110) REVERT: G 95 LYS cc_start: 0.8693 (ttmt) cc_final: 0.8491 (ttmm) REVERT: H 93 GLU cc_start: 0.8565 (mm-30) cc_final: 0.7675 (mm-30) REVERT: H 95 GLN cc_start: 0.8279 (tt0) cc_final: 0.7392 (tm-30) outliers start: 42 outliers final: 28 residues processed: 183 average time/residue: 0.2617 time to fit residues: 66.9157 Evaluate side-chains 187 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 157 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 111 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 63 optimal weight: 0.0980 chunk 85 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12810 Z= 0.214 Angle : 0.640 9.700 18535 Z= 0.363 Chirality : 0.034 0.172 2099 Planarity : 0.004 0.040 1338 Dihedral : 30.247 145.664 4015 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.47 % Allowed : 31.10 % Favored : 64.43 % 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: 0.63 (0.30), residues: 749 helix: 1.20 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -1.45 (0.34), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 47 HIS 0.005 0.001 HIS F 75 PHE 0.012 0.001 PHE E 67 TYR 0.065 0.003 TYR H 83 ARG 0.003 0.000 ARG E 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 170 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8581 (m-40) cc_final: 0.8115 (m-40) REVERT: A 110 TYR cc_start: 0.7640 (t80) cc_final: 0.6825 (t80) REVERT: A 128 LEU cc_start: 0.8293 (tt) cc_final: 0.8067 (tp) REVERT: B 24 ASP cc_start: 0.7915 (t0) cc_final: 0.7249 (p0) REVERT: B 44 LYS cc_start: 0.8441 (tttt) cc_final: 0.7936 (pttt) REVERT: B 45 ARG cc_start: 0.7525 (mtm180) cc_final: 0.6458 (ttm170) REVERT: B 51 TYR cc_start: 0.8050 (m-80) cc_final: 0.7636 (m-80) REVERT: B 79 LYS cc_start: 0.8473 (mtpp) cc_final: 0.7891 (mtmm) REVERT: B 84 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7101 (mtm) REVERT: B 92 ARG cc_start: 0.7779 (mmm-85) cc_final: 0.7174 (tpm170) REVERT: C 64 GLU cc_start: 0.8453 (tp30) cc_final: 0.8088 (mm-30) REVERT: D 59 MET cc_start: 0.8027 (tpp) cc_final: 0.7649 (tpp) REVERT: E 49 LYS cc_start: 0.8930 (ptmt) cc_final: 0.8710 (ptmt) REVERT: E 73 GLU cc_start: 0.9125 (tp30) cc_final: 0.8266 (tm-30) REVERT: E 99 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7541 (mm-30) REVERT: E 110 TYR cc_start: 0.7104 (t80) cc_final: 0.6722 (t80) REVERT: F 31 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7442 (tttm) REVERT: F 53 GLU cc_start: 0.8139 (tt0) cc_final: 0.7760 (tt0) REVERT: F 84 MET cc_start: 0.7718 (mmp) cc_final: 0.7507 (mmp) REVERT: G 71 ARG cc_start: 0.8759 (mmm-85) cc_final: 0.7802 (ptp-170) REVERT: H 93 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7826 (mm-30) REVERT: H 95 GLN cc_start: 0.8177 (tt0) cc_final: 0.7351 (tm-30) outliers start: 28 outliers final: 23 residues processed: 180 average time/residue: 0.2428 time to fit residues: 61.2327 Evaluate side-chains 188 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 163 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 20.0000 chunk 11 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 82 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 57 optimal weight: 0.0050 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** H 49 HIS ** 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 = 0.4275 r_free = 0.4275 target = 0.136404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.099857 restraints weight = 32929.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.103374 restraints weight = 16799.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.105746 restraints weight = 10807.928| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12810 Z= 0.175 Angle : 0.622 9.018 18535 Z= 0.350 Chirality : 0.034 0.162 2099 Planarity : 0.004 0.043 1338 Dihedral : 29.984 144.064 4015 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.35 % Allowed : 32.54 % Favored : 64.11 % 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: 0.99 (0.30), residues: 749 helix: 1.37 (0.23), residues: 532 sheet: None (None), residues: 0 loop : -1.09 (0.37), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP E 47 HIS 0.005 0.001 HIS F 75 PHE 0.011 0.001 PHE H 65 TYR 0.049 0.002 TYR H 83 ARG 0.003 0.000 ARG E 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2117.68 seconds wall clock time: 38 minutes 55.18 seconds (2335.18 seconds total)