Starting phenix.real_space_refine on Fri Mar 15 18:39:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6q_29778/03_2024/8g6q_29778_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6q_29778/03_2024/8g6q_29778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6q_29778/03_2024/8g6q_29778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6q_29778/03_2024/8g6q_29778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6q_29778/03_2024/8g6q_29778_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6q_29778/03_2024/8g6q_29778_neut.pdb" } resolution = 3.41 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= 0.001 sd= 0.011 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 13 5.16 5 C 6947 2.51 5 N 2331 2.21 5 O 2906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E ASP 77": "OD1" <-> "OD2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "H PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12485 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} 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} Chain: "K" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LEU K 73 " occ=0.63 ... (6 atoms not shown) pdb=" CD2 LEU K 73 " occ=0.63 Time building chain proxies: 6.67, per 1000 atoms: 0.53 Number of scatterers: 12485 At special positions: 0 Unit cell: (125.13, 83.42, 118.34, 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 13 16.00 P 288 15.00 O 2906 8.00 N 2331 7.00 C 6947 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 1.3 seconds 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1546 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 10 sheets defined 69.1% alpha, 4.2% beta 140 base pairs and 252 stacking pairs defined. Time for finding SS restraints: 4.70 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.988A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.576A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.578A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 50 through 76 Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.654A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 removed outlier: 3.600A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.598A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.807A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.806A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.640A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.630A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.540A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.565A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.675A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.644A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.537A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 72 removed outlier: 3.577A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.748A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.880A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 34 Processing helix chain 'K' and resid 55 through 60 removed outlier: 3.702A pdb=" N TYR K 59 " --> pdb=" O THR K 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.913A 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 removed outlier: 3.657A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.257A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.033A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.062A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.972A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (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 Processing sheet with id=AB1, first strand: chain 'K' and resid 12 through 16 415 hydrogen bonds defined for protein. 1233 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 357 hydrogen bonds 714 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 252 stacking parallelities Total time for adding SS restraints: 4.52 Time building geometry restraints manager: 6.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2851 1.34 - 1.46: 4008 1.46 - 1.58: 5834 1.58 - 1.70: 576 1.70 - 1.82: 24 Bond restraints: 13293 Sorted by residual: bond pdb=" N ALA E 114 " pdb=" CA ALA E 114 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.40e-02 5.10e+03 4.38e+00 bond pdb=" P DG J 12 " pdb=" OP2 DG J 12 " ideal model delta sigma weight residual 1.480 1.519 -0.039 2.00e-02 2.50e+03 3.82e+00 bond pdb=" P DT J 13 " pdb=" OP2 DT J 13 " ideal model delta sigma weight residual 1.480 1.517 -0.037 2.00e-02 2.50e+03 3.51e+00 bond pdb=" P DT J 14 " pdb=" OP2 DT J 14 " ideal model delta sigma weight residual 1.480 1.517 -0.037 2.00e-02 2.50e+03 3.39e+00 bond pdb=" P DT J 13 " pdb=" OP1 DT J 13 " ideal model delta sigma weight residual 1.480 1.516 -0.036 2.00e-02 2.50e+03 3.32e+00 ... (remaining 13288 not shown) Histogram of bond angle deviations from ideal: 98.43 - 105.24: 1241 105.24 - 112.05: 7358 112.05 - 118.87: 3347 118.87 - 125.68: 6270 125.68 - 132.49: 983 Bond angle restraints: 19199 Sorted by residual: angle pdb=" C3' DT J 13 " pdb=" O3' DT J 13 " pdb=" P DT J 14 " ideal model delta sigma weight residual 120.20 113.76 6.44 1.50e+00 4.44e-01 1.84e+01 angle pdb=" C3' DC J 11 " pdb=" O3' DC J 11 " pdb=" P DG J 12 " ideal model delta sigma weight residual 120.20 114.93 5.27 1.50e+00 4.44e-01 1.23e+01 angle pdb=" N ASN D 81 " pdb=" CA ASN D 81 " pdb=" C ASN D 81 " ideal model delta sigma weight residual 112.25 107.80 4.45 1.36e+00 5.41e-01 1.07e+01 angle pdb=" C3' DG J 12 " pdb=" O3' DG J 12 " pdb=" P DT J 13 " ideal model delta sigma weight residual 120.20 115.50 4.70 1.50e+00 4.44e-01 9.83e+00 angle pdb=" CA ASN D 81 " pdb=" CB ASN D 81 " pdb=" CG ASN D 81 " ideal model delta sigma weight residual 112.60 115.72 -3.12 1.00e+00 1.00e+00 9.71e+00 ... (remaining 19194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.03: 5833 35.03 - 70.06: 1405 70.06 - 105.09: 23 105.09 - 140.12: 5 140.12 - 175.15: 1 Dihedral angle restraints: 7267 sinusoidal: 4874 harmonic: 2393 Sorted by residual: 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 44.85 175.15 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA ILE K 44 " pdb=" C ILE K 44 " pdb=" N PHE K 45 " pdb=" CA PHE K 45 " ideal model delta harmonic sigma weight residual 180.00 161.20 18.80 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" C4' DC J 34 " pdb=" C3' DC J 34 " pdb=" O3' DC J 34 " pdb=" P DT J 35 " ideal model delta sinusoidal sigma weight residual 220.00 86.57 133.43 1 3.50e+01 8.16e-04 1.32e+01 ... (remaining 7264 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2143 0.094 - 0.188: 46 0.188 - 0.281: 2 0.281 - 0.375: 0 0.375 - 0.469: 3 Chirality restraints: 2194 Sorted by residual: chirality pdb=" P DG J 12 " pdb=" OP1 DG J 12 " pdb=" OP2 DG J 12 " pdb=" O5' DG J 12 " both_signs ideal model delta sigma weight residual True 2.35 -2.81 -0.47 2.00e-01 2.50e+01 5.50e+00 chirality pdb=" P DT J 13 " pdb=" OP1 DT J 13 " pdb=" OP2 DT J 13 " pdb=" O5' DT J 13 " both_signs ideal model delta sigma weight residual True 2.35 -2.81 -0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" P DT J 14 " pdb=" OP1 DT J 14 " pdb=" OP2 DT J 14 " pdb=" O5' DT J 14 " both_signs ideal model delta sigma weight residual True 2.35 -2.80 -0.45 2.00e-01 2.50e+01 5.07e+00 ... (remaining 2191 not shown) Planarity restraints: 1427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 81 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.13e+00 pdb=" C ASN D 81 " 0.039 2.00e-02 2.50e+03 pdb=" O ASN D 81 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS D 82 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 40 " 0.007 2.00e-02 2.50e+03 1.14e-02 2.92e+00 pdb=" N1 DC J 40 " -0.012 2.00e-02 2.50e+03 pdb=" C2 DC J 40 " 0.023 2.00e-02 2.50e+03 pdb=" O2 DC J 40 " -0.013 2.00e-02 2.50e+03 pdb=" N3 DC J 40 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DC J 40 " 0.013 2.00e-02 2.50e+03 pdb=" N4 DC J 40 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DC J 40 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC J 40 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 68 " 0.008 2.00e-02 2.50e+03 1.11e-02 2.75e+00 pdb=" N1 DC J 68 " -0.007 2.00e-02 2.50e+03 pdb=" C2 DC J 68 " 0.024 2.00e-02 2.50e+03 pdb=" O2 DC J 68 " -0.017 2.00e-02 2.50e+03 pdb=" N3 DC J 68 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DC J 68 " 0.007 2.00e-02 2.50e+03 pdb=" N4 DC J 68 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DC J 68 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DC J 68 " -0.005 2.00e-02 2.50e+03 ... (remaining 1424 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 639 2.71 - 3.26: 10948 3.26 - 3.81: 22761 3.81 - 4.35: 26747 4.35 - 4.90: 39308 Nonbonded interactions: 100403 Sorted by model distance: nonbonded pdb=" O ARG A 129 " pdb=" NH1 ARG A 129 " model vdw 2.164 2.520 nonbonded pdb=" N GLU F 52 " pdb=" OE1 GLU F 52 " model vdw 2.217 2.520 nonbonded pdb=" N GLU H 102 " pdb=" OE1 GLU H 102 " model vdw 2.218 2.520 nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 75 " model vdw 2.242 2.440 nonbonded pdb=" N GLU B 52 " pdb=" OE1 GLU B 52 " model vdw 2.257 2.520 ... (remaining 100398 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' and resid 39 through 135) selection = (chain 'E' and (resid 39 through 134 or (resid 135 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 29 through 121) 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=0.63 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 4.640 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 38.590 Find NCS groups from input model: 0.470 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: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 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 : 0.003 0.039 13293 Z= 0.188 Angle : 0.608 9.784 19199 Z= 0.352 Chirality : 0.037 0.469 2194 Planarity : 0.004 0.033 1427 Dihedral : 27.964 175.148 5721 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.14 % Allowed : 28.47 % Favored : 71.39 % 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: 2.17 (0.30), residues: 807 helix: 2.70 (0.23), residues: 523 sheet: -0.32 (1.11), residues: 24 loop : -1.13 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 113 PHE 0.007 0.001 PHE D 62 TYR 0.013 0.001 TYR A 54 ARG 0.008 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7836 (ttp-170) REVERT: B 91 LYS cc_start: 0.8766 (ttpt) cc_final: 0.8538 (tttt) REVERT: C 64 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8407 (tm-30) REVERT: C 99 ARG cc_start: 0.7172 (mtt180) cc_final: 0.5960 (mtp85) REVERT: E 64 LYS cc_start: 0.7944 (mttt) cc_final: 0.7521 (tmtt) REVERT: E 73 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8794 (tm-30) REVERT: G 95 LYS cc_start: 0.8244 (tmmt) cc_final: 0.7748 (tmmt) REVERT: K 1 MET cc_start: 0.4568 (tmm) cc_final: 0.2263 (pmm) REVERT: K 60 ASN cc_start: 0.8614 (m-40) cc_final: 0.8286 (m-40) outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.3014 time to fit residues: 64.4131 Evaluate side-chains 133 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 32 optimal weight: 0.3980 chunk 50 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13293 Z= 0.259 Angle : 0.584 5.664 19199 Z= 0.344 Chirality : 0.034 0.191 2194 Planarity : 0.004 0.044 1427 Dihedral : 29.976 176.308 4085 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.17 % Allowed : 28.03 % Favored : 69.80 % 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: 2.05 (0.31), residues: 807 helix: 2.70 (0.23), residues: 527 sheet: -0.49 (1.10), residues: 24 loop : -1.47 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS B 75 PHE 0.009 0.001 PHE B 61 TYR 0.012 0.002 TYR G 50 ARG 0.005 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7293 (pp) REVERT: B 35 ARG cc_start: 0.8218 (ttm-80) cc_final: 0.7851 (ttp-170) REVERT: B 91 LYS cc_start: 0.8863 (ttpt) cc_final: 0.8653 (ttmt) REVERT: C 64 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8455 (tm-30) REVERT: C 99 ARG cc_start: 0.7152 (mtt180) cc_final: 0.6007 (mtp-110) REVERT: D 81 ASN cc_start: 0.7590 (t0) cc_final: 0.7387 (t0) REVERT: E 64 LYS cc_start: 0.8134 (mttt) cc_final: 0.7701 (tmtt) REVERT: G 64 GLU cc_start: 0.7865 (tt0) cc_final: 0.7549 (tm-30) REVERT: K 1 MET cc_start: 0.4953 (tmm) cc_final: 0.3876 (ppp) REVERT: K 60 ASN cc_start: 0.8659 (m-40) cc_final: 0.8331 (m-40) outliers start: 15 outliers final: 8 residues processed: 146 average time/residue: 0.3044 time to fit residues: 60.1140 Evaluate side-chains 137 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 5 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 96 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 64 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13293 Z= 0.332 Angle : 0.609 6.502 19199 Z= 0.360 Chirality : 0.036 0.149 2194 Planarity : 0.005 0.048 1427 Dihedral : 29.928 176.387 4085 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.62 % Allowed : 25.72 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.30), residues: 807 helix: 2.38 (0.22), residues: 531 sheet: -0.80 (1.04), residues: 24 loop : -1.56 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS B 75 PHE 0.009 0.002 PHE B 61 TYR 0.012 0.002 TYR E 41 ARG 0.004 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 131 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8109 (ttm-80) cc_final: 0.7760 (ttp-170) REVERT: B 53 GLU cc_start: 0.8828 (mp0) cc_final: 0.8570 (mp0) REVERT: B 91 LYS cc_start: 0.8915 (ttpt) cc_final: 0.8681 (ttmt) REVERT: C 64 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8417 (tm-30) REVERT: C 99 ARG cc_start: 0.7169 (mtt180) cc_final: 0.6087 (mtp85) REVERT: D 81 ASN cc_start: 0.7972 (t0) cc_final: 0.7716 (t0) REVERT: E 60 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7852 (mt) REVERT: E 64 LYS cc_start: 0.8118 (mttt) cc_final: 0.7709 (tmtt) REVERT: K 1 MET cc_start: 0.5394 (tmm) cc_final: 0.2651 (pmm) REVERT: K 60 ASN cc_start: 0.8683 (m-40) cc_final: 0.8371 (m-40) outliers start: 32 outliers final: 24 residues processed: 156 average time/residue: 0.2706 time to fit residues: 57.8576 Evaluate side-chains 147 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 102 optimal weight: 40.0000 chunk 91 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 55 GLN E 125 GLN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13293 Z= 0.302 Angle : 0.595 6.444 19199 Z= 0.352 Chirality : 0.035 0.149 2194 Planarity : 0.004 0.048 1427 Dihedral : 29.923 176.638 4085 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.77 % Allowed : 26.30 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.30), residues: 807 helix: 2.47 (0.22), residues: 532 sheet: -0.84 (1.02), residues: 24 loop : -1.63 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 75 PHE 0.011 0.001 PHE H 67 TYR 0.016 0.002 TYR D 80 ARG 0.004 0.000 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 126 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8151 (tp40) cc_final: 0.7938 (tp-100) REVERT: B 35 ARG cc_start: 0.8107 (ttm-80) cc_final: 0.7780 (mtm180) REVERT: B 52 GLU cc_start: 0.8588 (mp0) cc_final: 0.8325 (mp0) REVERT: B 53 GLU cc_start: 0.8895 (mp0) cc_final: 0.8491 (mp0) REVERT: C 64 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8405 (tm-30) REVERT: C 99 ARG cc_start: 0.7253 (mtt180) cc_final: 0.6239 (mtp85) REVERT: D 81 ASN cc_start: 0.7991 (t0) cc_final: 0.7685 (t0) REVERT: E 60 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7846 (mt) REVERT: E 64 LYS cc_start: 0.8098 (mttt) cc_final: 0.7687 (tmtt) REVERT: H 31 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7015 (pttm) REVERT: H 73 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8337 (mm-30) REVERT: K 1 MET cc_start: 0.5308 (tmm) cc_final: 0.2466 (pmm) REVERT: K 68 HIS cc_start: 0.8826 (t70) cc_final: 0.8599 (t70) outliers start: 33 outliers final: 25 residues processed: 152 average time/residue: 0.2766 time to fit residues: 57.5345 Evaluate side-chains 149 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 122 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13293 Z= 0.210 Angle : 0.555 6.847 19199 Z= 0.332 Chirality : 0.033 0.143 2194 Planarity : 0.004 0.047 1427 Dihedral : 29.864 177.025 4085 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.90 % Allowed : 27.31 % Favored : 68.79 % 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: 2.03 (0.31), residues: 807 helix: 2.71 (0.22), residues: 532 sheet: -0.96 (1.01), residues: 25 loop : -1.59 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS B 75 PHE 0.011 0.001 PHE H 67 TYR 0.017 0.002 TYR H 80 ARG 0.003 0.000 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 133 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8127 (ttm-80) cc_final: 0.7852 (mtm180) REVERT: B 52 GLU cc_start: 0.8508 (mp0) cc_final: 0.8284 (mp0) REVERT: B 53 GLU cc_start: 0.8930 (mp0) cc_final: 0.8506 (mp0) REVERT: C 64 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8361 (tm-30) REVERT: C 99 ARG cc_start: 0.7291 (mtt180) cc_final: 0.6340 (mtp85) REVERT: D 81 ASN cc_start: 0.7776 (t0) cc_final: 0.7473 (t0) REVERT: E 60 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7849 (mt) REVERT: G 64 GLU cc_start: 0.7877 (tt0) cc_final: 0.7586 (tm-30) REVERT: H 31 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.6998 (pttm) REVERT: H 73 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8336 (mm-30) REVERT: K 1 MET cc_start: 0.5420 (tmm) cc_final: 0.2763 (pmm) REVERT: K 68 HIS cc_start: 0.8773 (t70) cc_final: 0.8510 (t70) outliers start: 27 outliers final: 20 residues processed: 157 average time/residue: 0.2710 time to fit residues: 58.5009 Evaluate side-chains 148 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13293 Z= 0.182 Angle : 0.549 7.479 19199 Z= 0.326 Chirality : 0.033 0.161 2194 Planarity : 0.004 0.045 1427 Dihedral : 29.826 178.232 4085 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.48 % Allowed : 27.60 % Favored : 67.92 % 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: 2.18 (0.31), residues: 807 helix: 2.79 (0.22), residues: 532 sheet: -0.98 (0.99), residues: 25 loop : -1.43 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 75 PHE 0.012 0.001 PHE H 67 TYR 0.011 0.001 TYR D 80 ARG 0.003 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 135 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8132 (ttm-80) cc_final: 0.7858 (mtm180) REVERT: B 52 GLU cc_start: 0.8560 (mp0) cc_final: 0.8359 (mp0) REVERT: B 53 GLU cc_start: 0.8975 (mp0) cc_final: 0.8531 (mp0) REVERT: C 64 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8353 (tm-30) REVERT: C 99 ARG cc_start: 0.7281 (mtt180) cc_final: 0.6249 (mtp85) REVERT: D 81 ASN cc_start: 0.7676 (t0) cc_final: 0.7398 (t0) REVERT: E 60 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7791 (mt) REVERT: E 125 GLN cc_start: 0.8382 (mt0) cc_final: 0.8165 (mt0) REVERT: G 64 GLU cc_start: 0.7849 (tt0) cc_final: 0.7617 (tm-30) REVERT: H 31 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.6984 (ptpp) REVERT: H 73 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8335 (tp30) REVERT: K 1 MET cc_start: 0.5308 (tmm) cc_final: 0.2597 (pmm) outliers start: 31 outliers final: 19 residues processed: 161 average time/residue: 0.2756 time to fit residues: 60.8454 Evaluate side-chains 151 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13293 Z= 0.319 Angle : 0.611 7.983 19199 Z= 0.358 Chirality : 0.036 0.154 2194 Planarity : 0.004 0.046 1427 Dihedral : 29.874 179.299 4085 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.91 % Allowed : 26.88 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.30), residues: 807 helix: 2.57 (0.22), residues: 533 sheet: -0.52 (1.11), residues: 19 loop : -1.57 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS B 75 PHE 0.009 0.002 PHE B 61 TYR 0.024 0.002 TYR D 80 ARG 0.004 0.000 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 127 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8102 (ttm-80) cc_final: 0.7826 (mtm180) REVERT: B 52 GLU cc_start: 0.8574 (mp0) cc_final: 0.8331 (mp0) REVERT: B 53 GLU cc_start: 0.9012 (mp0) cc_final: 0.8468 (mp0) REVERT: C 64 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8384 (tm-30) REVERT: C 99 ARG cc_start: 0.7298 (mtt180) cc_final: 0.6266 (mtp85) REVERT: D 81 ASN cc_start: 0.7994 (t0) cc_final: 0.7706 (t0) REVERT: E 60 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7863 (mt) REVERT: E 64 LYS cc_start: 0.8158 (mttt) cc_final: 0.7757 (tmtt) REVERT: H 31 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.6967 (ptpp) REVERT: H 48 ASP cc_start: 0.9153 (p0) cc_final: 0.8950 (p0) REVERT: K 1 MET cc_start: 0.5560 (tmm) cc_final: 0.2978 (pmm) outliers start: 34 outliers final: 26 residues processed: 156 average time/residue: 0.2815 time to fit residues: 60.3284 Evaluate side-chains 151 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 123 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13293 Z= 0.181 Angle : 0.559 9.497 19199 Z= 0.330 Chirality : 0.033 0.144 2194 Planarity : 0.004 0.045 1427 Dihedral : 29.822 178.843 4085 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.18 % Allowed : 28.03 % Favored : 68.79 % 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: 2.23 (0.31), residues: 807 helix: 2.81 (0.22), residues: 533 sheet: -0.95 (0.97), residues: 25 loop : -1.38 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 75 PHE 0.012 0.001 PHE H 67 TYR 0.013 0.001 TYR D 80 ARG 0.005 0.000 ARG K 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8136 (ttm-80) cc_final: 0.7874 (mtm180) REVERT: B 52 GLU cc_start: 0.8548 (mp0) cc_final: 0.8338 (mp0) REVERT: B 53 GLU cc_start: 0.8988 (mp0) cc_final: 0.8530 (mp0) REVERT: C 64 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8354 (tm-30) REVERT: C 99 ARG cc_start: 0.7283 (mtt180) cc_final: 0.6408 (mtp-110) REVERT: D 81 ASN cc_start: 0.7701 (t0) cc_final: 0.7467 (t0) REVERT: E 60 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7780 (mt) REVERT: H 31 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.6972 (pttp) REVERT: H 73 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8354 (tp30) REVERT: K 1 MET cc_start: 0.5408 (tmm) cc_final: 0.2904 (pmm) outliers start: 22 outliers final: 17 residues processed: 156 average time/residue: 0.2851 time to fit residues: 60.6817 Evaluate side-chains 150 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 131 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 62 optimal weight: 0.4980 chunk 100 optimal weight: 10.0000 overall best weight: 4.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.051 13293 Z= 0.526 Angle : 0.726 8.589 19199 Z= 0.419 Chirality : 0.043 0.315 2194 Planarity : 0.006 0.050 1427 Dihedral : 29.995 179.141 4085 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 5.06 % Allowed : 26.30 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.30), residues: 807 helix: 2.03 (0.22), residues: 533 sheet: 0.14 (1.20), residues: 17 loop : -1.69 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS B 75 PHE 0.012 0.002 PHE H 62 TYR 0.047 0.003 TYR D 80 ARG 0.005 0.001 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 129 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8128 (ttm-80) cc_final: 0.7855 (mtm180) REVERT: B 52 GLU cc_start: 0.8699 (mp0) cc_final: 0.8301 (mp0) REVERT: B 53 GLU cc_start: 0.9045 (mp0) cc_final: 0.8482 (mp0) REVERT: C 64 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8368 (tm-30) REVERT: C 99 ARG cc_start: 0.7246 (mtt180) cc_final: 0.6275 (mtp85) REVERT: D 81 ASN cc_start: 0.8066 (t0) cc_final: 0.7828 (t0) REVERT: E 60 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7907 (mt) REVERT: E 64 LYS cc_start: 0.8339 (mttt) cc_final: 0.7948 (tmtt) REVERT: G 95 LYS cc_start: 0.8639 (tmmt) cc_final: 0.8296 (tmmt) REVERT: G 112 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7912 (mp10) REVERT: H 30 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7942 (mtp85) REVERT: H 31 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7004 (ptpp) REVERT: H 82 LYS cc_start: 0.9410 (tptp) cc_final: 0.9100 (tptp) REVERT: K 1 MET cc_start: 0.5863 (tmm) cc_final: 0.3413 (pmm) outliers start: 35 outliers final: 26 residues processed: 157 average time/residue: 0.2943 time to fit residues: 62.5776 Evaluate side-chains 151 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 121 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.7980 chunk 47 optimal weight: 0.0870 chunk 69 optimal weight: 0.5980 chunk 105 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13293 Z= 0.189 Angle : 0.585 10.864 19199 Z= 0.344 Chirality : 0.035 0.193 2194 Planarity : 0.004 0.044 1427 Dihedral : 29.907 178.875 4085 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.75 % Allowed : 28.90 % Favored : 68.35 % 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: 2.02 (0.31), residues: 807 helix: 2.64 (0.22), residues: 536 sheet: -0.68 (1.06), residues: 22 loop : -1.56 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS B 75 PHE 0.013 0.001 PHE H 67 TYR 0.012 0.001 TYR D 37 ARG 0.004 0.000 ARG B 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8139 (ttm-80) cc_final: 0.7879 (mtm180) REVERT: B 52 GLU cc_start: 0.8498 (mp0) cc_final: 0.8275 (mp0) REVERT: B 53 GLU cc_start: 0.9019 (mp0) cc_final: 0.8543 (mp0) REVERT: C 64 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8361 (tm-30) REVERT: C 99 ARG cc_start: 0.7202 (mtt180) cc_final: 0.6207 (mtp85) REVERT: D 81 ASN cc_start: 0.7794 (t0) cc_final: 0.7589 (t0) REVERT: G 95 LYS cc_start: 0.8562 (tmmt) cc_final: 0.8042 (tmmt) REVERT: H 30 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7818 (mtt90) REVERT: H 31 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7009 (pttp) REVERT: H 73 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8318 (tp30) REVERT: K 1 MET cc_start: 0.5702 (tmm) cc_final: 0.3164 (pmm) outliers start: 19 outliers final: 16 residues processed: 154 average time/residue: 0.2908 time to fit residues: 61.0166 Evaluate side-chains 153 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 10 optimal weight: 0.0040 chunk 15 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.098917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.066781 restraints weight = 32765.291| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.68 r_work: 0.2848 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13293 Z= 0.192 Angle : 0.580 11.152 19199 Z= 0.340 Chirality : 0.034 0.170 2194 Planarity : 0.004 0.044 1427 Dihedral : 29.884 178.933 4085 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.46 % Allowed : 29.48 % Favored : 68.06 % 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: 2.10 (0.31), residues: 807 helix: 2.71 (0.22), residues: 533 sheet: -0.59 (1.08), residues: 22 loop : -1.46 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 75 PHE 0.011 0.001 PHE H 67 TYR 0.017 0.001 TYR D 80 ARG 0.002 0.000 ARG G 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2278.49 seconds wall clock time: 42 minutes 6.89 seconds (2526.89 seconds total)