Starting phenix.real_space_refine on Mon Oct 26 17:28:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r94_4768/10_2026/6r94_4768.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r94_4768/10_2026/6r94_4768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6r94_4768/10_2026/6r94_4768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r94_4768/10_2026/6r94_4768.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6r94_4768/10_2026/6r94_4768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r94_4768/10_2026/6r94_4768.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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: 6 Type Number sf(0) Gaussians P 292 5.49 5 S 14 5.16 5 C 6879 2.51 5 N 2316 2.21 5 O 2871 1.98 5 H 10071 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22443 Number of models: 1 Model: "" Number of chains: 10 Chain: "I" Number of atoms: 4649 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 145, 4611 Classifications: {'DNA': 145} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 144} Conformer: "B" Number of residues, atoms: 145, 4584 Classifications: {'DNA': 145} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 144} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 4900 Chain: "J" Number of atoms: 4646 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 145, 4581 Classifications: {'DNA': 145} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 144} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 145, 4608 Classifications: {'DNA': 145} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 144} bond proxies already assigned to first conformer: 4898 Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1705 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "B" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1394 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 1831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1831 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "D" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1559 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1707 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "F" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1456 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "H" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1611 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 97} Residues with excluded nonbonded symmetry interactions: 4 residue group: pdb=" P A DG I 97 " occ=0.50 ... (50 atoms not shown) pdb="H4'1B3DR I 97 " occ=0.50 residue group: pdb=" P A DA I 98 " occ=0.50 ... (49 atoms not shown) pdb="H4'1B3DR I 98 " occ=0.50 residue group: pdb=" P A3DR J 97 " occ=0.50 ... (50 atoms not shown) pdb=" H22B DG J 97 " occ=0.50 residue group: pdb=" P A3DR J 98 " occ=0.50 ... (49 atoms not shown) pdb=" H2 B DA J 98 " occ=0.50 Time building chain proxies: 5.37, per 1000 atoms: 0.24 Number of scatterers: 22443 At special positions: 0 Unit cell: (124.7, 103.2, 129.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 14 16.00 P 292 15.00 O 2871 8.00 N 2316 7.00 C 6879 6.00 H 10071 1.00 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 427.0 milliseconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1496 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 69.4% alpha, 3.0% beta 141 base pairs and 241 stacking pairs defined. Time for finding SS restraints: 3.77 Creating SS restraints... Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 64 through 78 removed outlier: 3.500A pdb=" N PHE A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 115 Processing helix chain 'A' and resid 121 through 133 removed outlier: 3.599A pdb=" N ILE A 125 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 78 removed outlier: 3.773A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 28 through 37 Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.375A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.551A pdb=" N LEU C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 35 through 47 Processing helix chain 'D' and resid 53 through 82 Processing helix chain 'D' and resid 88 through 100 removed outlier: 3.537A pdb=" N ILE D 92 " --> pdb=" O THR D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 122 removed outlier: 3.887A pdb=" N LYS D 106 " --> pdb=" O GLY D 102 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 64 through 80 removed outlier: 3.634A pdb=" N PHE E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE E 79 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 133 removed outlier: 3.506A pdb=" N ILE E 125 " --> pdb=" O MET E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 removed outlier: 3.784A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.573A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.464A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 90 removed outlier: 3.581A pdb=" N LEU G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 125 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.525A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 removed outlier: 3.608A pdb=" N ILE A 120 " --> pdb=" O ARG B 46 " (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 99 removed outlier: 6.807A pdb=" N THR B 97 " --> pdb=" O THR G 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.471A pdb=" N ARG C 43 " --> pdb=" O ILE D 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 removed outlier: 3.766A pdb=" N ILE C 79 " --> pdb=" O GLY D 51 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103 removed outlier: 6.533A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 7.438A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 removed outlier: 3.565A pdb=" N ILE E 120 " --> pdb=" O ARG F 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.378A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 removed outlier: 3.762A pdb=" N ILE G 79 " --> pdb=" O GLY H 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 401 hydrogen bonds defined for protein. 1179 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for 3DR residue (no planarity definition) Warning, Cannot make NA restraints for 3DR residue (no planarity definition) Warning, Cannot make NA restraints for 3DR residue (no planarity definition) Warning, Cannot make NA restraints for 3DR residue (no planarity definition) Warning, Cannot make NA restraints for 3DR residue (no planarity definition) Warning, Cannot make NA restraints for 3DR residue (no planarity definition) Warning, Cannot make NA restraints for 3DR residue (no planarity definition) Restraints generated for nucleic acids: 339 hydrogen bonds 678 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 241 stacking parallelities Total time for adding SS restraints: 5.05 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 10035 1.03 - 1.22: 125 1.22 - 1.42: 5546 1.42 - 1.61: 7517 1.61 - 1.81: 32 Bond restraints: 23255 Sorted by residual: bond pdb=" P A3DR J 98 " pdb=" O5'A3DR J 98 " ideal model delta sigma weight residual 1.720 1.600 0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" C5'A3DR J 98 " pdb=" H5'A3DR J 98 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" C1' DC J 13 " pdb=" N1 DC J 13 " ideal model delta sigma weight residual 1.468 1.552 -0.084 1.40e-02 5.10e+03 3.58e+01 bond pdb=" C2'A3DR J 97 " pdb="H2''A3DR J 97 " ideal model delta sigma weight residual 0.970 1.089 -0.119 2.00e-02 2.50e+03 3.57e+01 bond pdb=" C2'A3DR J 97 " pdb=" H2'A3DR J 97 " ideal model delta sigma weight residual 0.970 1.089 -0.119 2.00e-02 2.50e+03 3.57e+01 ... (remaining 23250 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.61: 42165 5.61 - 11.22: 45 11.22 - 16.82: 1 16.82 - 22.43: 0 22.43 - 28.04: 6 Bond angle restraints: 42217 Sorted by residual: angle pdb=" C SER H 33 " pdb=" CA SER H 33 " pdb=" HA SER H 33 " ideal model delta sigma weight residual 109.00 80.96 28.04 3.00e+00 1.11e-01 8.74e+01 angle pdb=" CB SER H 33 " pdb=" CA SER H 33 " pdb=" HA SER H 33 " ideal model delta sigma weight residual 109.00 82.20 26.80 3.00e+00 1.11e-01 7.98e+01 angle pdb=" CG1 VAL A 36 " pdb=" CB VAL A 36 " pdb=" HB VAL A 36 " ideal model delta sigma weight residual 108.00 81.81 26.19 3.00e+00 1.11e-01 7.62e+01 angle pdb=" CG2 VAL A 36 " pdb=" CB VAL A 36 " pdb=" HB VAL A 36 " ideal model delta sigma weight residual 108.00 82.04 25.96 3.00e+00 1.11e-01 7.49e+01 angle pdb=" N SER H 33 " pdb=" CA SER H 33 " pdb=" HA SER H 33 " ideal model delta sigma weight residual 110.00 84.53 25.47 3.00e+00 1.11e-01 7.21e+01 ... (remaining 42212 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 8427 35.99 - 71.98: 1382 71.98 - 107.97: 21 107.97 - 143.96: 12 143.96 - 179.95: 7 Dihedral angle restraints: 9849 sinusoidal: 7280 harmonic: 2569 Sorted by residual: dihedral pdb=" C SER H 33 " pdb=" N SER H 33 " pdb=" CA SER H 33 " pdb=" CB SER H 33 " ideal model delta harmonic sigma weight residual -122.60 -155.65 33.05 0 2.50e+00 1.60e-01 1.75e+02 dihedral pdb=" N SER H 33 " pdb=" C SER H 33 " pdb=" CA SER H 33 " pdb=" CB SER H 33 " ideal model delta harmonic sigma weight residual 122.80 153.93 -31.13 0 2.50e+00 1.60e-01 1.55e+02 dihedral pdb=" CA GLU E 134 " pdb=" C GLU E 134 " pdb=" N ARG E 135 " pdb=" CA ARG E 135 " ideal model delta harmonic sigma weight residual -180.00 -156.03 -23.97 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 9846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.285: 2152 0.285 - 0.571: 0 0.571 - 0.856: 0 0.856 - 1.141: 0 1.141 - 1.426: 2 Chirality restraints: 2154 Sorted by residual: chirality pdb=" CB VAL A 36 " pdb=" CA VAL A 36 " pdb=" CG1 VAL A 36 " pdb=" CG2 VAL A 36 " both_signs ideal model delta sigma weight residual False -2.63 -1.20 -1.43 2.00e-01 2.50e+01 5.09e+01 chirality pdb=" CA SER H 33 " pdb=" N SER H 33 " pdb=" C SER H 33 " pdb=" CB SER H 33 " both_signs ideal model delta sigma weight residual False 2.51 1.14 1.37 2.00e-01 2.50e+01 4.72e+01 chirality pdb=" CG LEU D 78 " pdb=" CB LEU D 78 " pdb=" CD1 LEU D 78 " pdb=" CD2 LEU D 78 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 2151 not shown) Planarity restraints: 2369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA H 125 " 0.037 2.00e-02 2.50e+03 7.25e-02 5.25e+01 pdb=" C ALA H 125 " -0.125 2.00e-02 2.50e+03 pdb=" O ALA H 125 " 0.047 2.00e-02 2.50e+03 pdb=" N LYS H 126 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 135 " -0.036 2.00e-02 2.50e+03 7.04e-02 4.95e+01 pdb=" C ARG E 135 " 0.122 2.00e-02 2.50e+03 pdb=" O ARG E 135 " -0.045 2.00e-02 2.50e+03 pdb=" N ALA E 136 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 135 " 0.034 2.00e-02 2.50e+03 6.78e-02 4.60e+01 pdb=" C ARG A 135 " -0.117 2.00e-02 2.50e+03 pdb=" O ARG A 135 " 0.044 2.00e-02 2.50e+03 pdb=" N ALA A 136 " 0.039 2.00e-02 2.50e+03 ... (remaining 2366 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 3048 2.26 - 2.85: 42435 2.85 - 3.43: 53719 3.43 - 4.02: 79923 4.02 - 4.60: 115993 Nonbonded interactions: 295118 Sorted by model distance: nonbonded pdb=" OD1 ASN F 65 " pdb="HH22 ARG F 68 " model vdw 1.680 2.450 nonbonded pdb=" OD2 ASP D 66 " pdb=" HH TYR F 99 " model vdw 1.705 2.450 nonbonded pdb="HH12 ARG G 82 " pdb=" O VAL G 108 " model vdw 1.728 2.450 nonbonded pdb=" OP1 DG J 68 " pdb="HH21 ARG E 43 " model vdw 1.742 2.450 nonbonded pdb=" OP2 DT J 52 " pdb=" HZ3 LYS F 21 " model vdw 1.745 2.450 ... (remaining 295113 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and (resid 36 through 128 or (resid 129 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG \ 3 or name HD2 or name HD3 or name HE or name HH21 or name HH22)) or resid 130 th \ rough 136)) } ncs_group { reference = chain 'B' selection = (chain 'F' and ((resid 20 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name H \ E or name HH11 or name HH12 or name HH21 or name HH22)) or resid 21 through 103) \ ) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 9 through 123) } ncs_group { reference = chain 'D' selection = (chain 'H' and ((resid 30 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name H \ E or name HH11 or name HH12 or name HH21 or name HH22)) or resid 31 through 123 \ or (resid 124 and (name N or name CA or name C or name O or name CB or name OG o \ r name HA or name HB2 or name HB3 or name HG )) or resid 125 through 126)) } ncs_group { reference = (chain 'I' and (resid 1 through 71 or resid 75 through 96 or resid 99 through 14 \ 5)) selection = (chain 'J' and (resid 1 through 71 or resid 75 through 96 or resid 99 through 14 \ 5)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 25.060 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 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 : 0.012 0.120 13184 Z= 0.750 Angle : 1.138 12.473 19037 Z= 0.893 Chirality : 0.082 1.426 2154 Planarity : 0.008 0.072 1395 Dihedral : 26.388 175.766 5854 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.05 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.26), residues: 787 helix: 0.84 (0.20), residues: 521 sheet: None (None), residues: 0 loop : -1.01 (0.31), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.003 ARG D 77 TYR 0.027 0.006 TYR A 100 PHE 0.021 0.003 PHE D 63 HIS 0.016 0.003 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.01152 / 0.75 (13184) covalent geometry : angle 1.13783 / 0.89 (19037) hydrogen bonds : bond 0.12555 / 13.68 ( 740) hydrogen bonds : angle 4.17030 / 5.47 ( 1857) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8748 (mttt) cc_final: 0.8531 (mtpp) REVERT: D 120 THR cc_start: 0.8269 (t) cc_final: 0.7975 (p) REVERT: G 74 ASN cc_start: 0.6138 (m-40) cc_final: 0.5724 (m-40) REVERT: G 76 LYS cc_start: 0.8026 (mttt) cc_final: 0.7818 (mmtm) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.3737 time to fit residues: 26.1866 Evaluate side-chains 50 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 100, 38, 61] chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.168917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.126040 restraints weight = 49489.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.132580 restraints weight = 19285.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.136745 restraints weight = 11692.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.138990 restraints weight = 9063.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.140310 restraints weight = 7991.497| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3890 r_free = 0.3890 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3888 r_free = 0.3888 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.3888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13184 Z= 0.190 Angle : 0.702 10.914 19037 Z= 0.449 Chirality : 0.053 1.417 2154 Planarity : 0.004 0.036 1395 Dihedral : 29.069 178.726 4232 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.30 % Allowed : 4.64 % Favored : 95.06 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.29), residues: 787 helix: 2.35 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -0.82 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 93 TYR 0.016 0.001 TYR A 100 PHE 0.008 0.001 PHE H 66 HIS 0.007 0.002 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.19 (13184) covalent geometry : angle 0.70194 / 0.45 (19037) hydrogen bonds : bond 0.08051 / 8.91 ( 740) hydrogen bonds : angle 3.40860 / 4.35 ( 1857) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.443 Fit side-chains REVERT: A 116 LYS cc_start: 0.8645 (mttt) cc_final: 0.8423 (mmmm) REVERT: C 42 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6653 (mt-10) REVERT: G 74 ASN cc_start: 0.6102 (m-40) cc_final: 0.5768 (m-40) REVERT: G 76 LYS cc_start: 0.8114 (mttt) cc_final: 0.7910 (mmtm) outliers start: 2 outliers final: 1 residues processed: 55 average time/residue: 0.3996 time to fit residues: 27.8651 Evaluate side-chains 54 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [78, 19, 60, 80, 74, 22, 102, 52, 42, 14, 43] chunk 78 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.165450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.123508 restraints weight = 46751.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.129211 restraints weight = 18803.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.132712 restraints weight = 11734.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.134621 restraints weight = 9334.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.135658 restraints weight = 8321.545| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3831 r_free = 0.3831 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3831 r_free = 0.3831 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13184 Z= 0.203 Angle : 0.657 10.769 19037 Z= 0.425 Chirality : 0.052 1.405 2154 Planarity : 0.004 0.055 1395 Dihedral : 29.183 175.057 4232 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.92 % Favored : 96.95 % Rotamer: Outliers : 0.60 % Allowed : 6.14 % Favored : 93.26 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.29), residues: 787 helix: 2.68 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.87 (0.34), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 93 TYR 0.016 0.001 TYR A 100 PHE 0.009 0.001 PHE B 101 HIS 0.006 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.20 (13184) covalent geometry : angle 0.65744 / 0.43 (19037) hydrogen bonds : bond 0.06999 / 7.72 ( 740) hydrogen bonds : angle 3.12018 / 3.96 ( 1857) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.443 Fit side-chains REVERT: A 132 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7387 (mtt180) REVERT: C 42 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6683 (mt-10) outliers start: 4 outliers final: 3 residues processed: 60 average time/residue: 0.4468 time to fit residues: 33.4423 Evaluate side-chains 60 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 83 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [93, 67, 77, 54, 15, 99, 23, 83, 104, 79, 61] chunk 93 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.164999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.121671 restraints weight = 52899.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.127660 restraints weight = 20006.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.131414 restraints weight = 12068.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.133473 restraints weight = 9414.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.134570 restraints weight = 8329.382| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3812 r_free = 0.3812 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3812 r_free = 0.3812 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13184 Z= 0.178 Angle : 0.626 10.869 19037 Z= 0.406 Chirality : 0.051 1.411 2154 Planarity : 0.004 0.042 1395 Dihedral : 29.234 175.467 4232 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.60 % Allowed : 6.44 % Favored : 92.96 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.29), residues: 787 helix: 2.75 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.02 (0.34), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 41 TYR 0.013 0.001 TYR A 100 PHE 0.005 0.001 PHE D 63 HIS 0.004 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.18 (13184) covalent geometry : angle 0.62588 / 0.41 (19037) hydrogen bonds : bond 0.06455 / 7.10 ( 740) hydrogen bonds : angle 2.99262 / 3.79 ( 1857) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7521 (mtt-85) REVERT: G 74 ASN cc_start: 0.5735 (m110) cc_final: 0.5480 (m-40) outliers start: 4 outliers final: 3 residues processed: 61 average time/residue: 0.4225 time to fit residues: 32.1416 Evaluate side-chains 59 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 83 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [54, 86, 62, 67, 80, 11, 69, 29, 4, 34, 48] chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.162607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.118854 restraints weight = 51808.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.124609 restraints weight = 20219.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.128233 restraints weight = 12440.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.130245 restraints weight = 9784.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.131148 restraints weight = 8686.633| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3765 r_free = 0.3765 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3765 r_free = 0.3765 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13184 Z= 0.212 Angle : 0.638 10.853 19037 Z= 0.411 Chirality : 0.051 1.405 2154 Planarity : 0.004 0.046 1395 Dihedral : 29.282 174.208 4232 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.94 % Favored : 95.93 % Rotamer: Outliers : 0.60 % Allowed : 6.59 % Favored : 92.81 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.29), residues: 787 helix: 2.66 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.02 (0.34), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 93 TYR 0.016 0.002 TYR A 100 PHE 0.006 0.001 PHE E 79 HIS 0.009 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.21 (13184) covalent geometry : angle 0.63765 / 0.41 (19037) hydrogen bonds : bond 0.06492 / 7.10 ( 740) hydrogen bonds : angle 2.98732 / 3.77 ( 1857) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.7697 (tttp) cc_final: 0.7432 (tttt) REVERT: A 132 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7617 (mtt-85) REVERT: B 93 ARG cc_start: 0.7670 (mtp-110) cc_final: 0.7126 (ttp80) REVERT: C 74 ASN cc_start: 0.7132 (t160) cc_final: 0.6932 (t0) REVERT: G 74 ASN cc_start: 0.5740 (m110) cc_final: 0.5484 (m-40) outliers start: 4 outliers final: 3 residues processed: 62 average time/residue: 0.4419 time to fit residues: 34.0009 Evaluate side-chains 64 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 83 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [20, 44, 103, 28, 77, 38, 35, 30, 12, 96, 84] chunk 20 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.162958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.119235 restraints weight = 49495.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.124980 restraints weight = 19819.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.128568 restraints weight = 12365.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.130349 restraints weight = 9792.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.131528 restraints weight = 8801.663| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3779 r_free = 0.3779 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3779 r_free = 0.3779 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13184 Z= 0.168 Angle : 0.604 10.863 19037 Z= 0.394 Chirality : 0.050 1.408 2154 Planarity : 0.004 0.046 1395 Dihedral : 29.293 174.689 4232 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.90 % Allowed : 6.89 % Favored : 92.22 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.30), residues: 787 helix: 2.82 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.08 (0.34), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 73 TYR 0.013 0.001 TYR A 100 PHE 0.005 0.001 PHE D 63 HIS 0.004 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.17 (13184) covalent geometry : angle 0.60415 / 0.39 (19037) hydrogen bonds : bond 0.06051 / 6.62 ( 740) hydrogen bonds : angle 2.88030 / 3.62 ( 1857) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7581 (mtt-85) REVERT: B 93 ARG cc_start: 0.7671 (mtp-110) cc_final: 0.7182 (ttp80) REVERT: C 74 ASN cc_start: 0.7214 (t160) cc_final: 0.6838 (t0) REVERT: G 36 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7352 (mtm-85) REVERT: G 74 ASN cc_start: 0.5670 (m110) cc_final: 0.5420 (m-40) outliers start: 6 outliers final: 4 residues processed: 60 average time/residue: 0.4354 time to fit residues: 32.6044 Evaluate side-chains 64 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 36 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [61, 68, 2, 57, 63, 95, 21, 1, 52, 103, 42] chunk 61 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 63 optimal weight: 0.3980 chunk 95 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.161788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.117649 restraints weight = 51260.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.123341 restraints weight = 20435.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.126885 restraints weight = 12710.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.128760 restraints weight = 10082.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.129894 restraints weight = 9013.937| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3754 r_free = 0.3754 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3754 r_free = 0.3754 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13184 Z= 0.194 Angle : 0.620 10.864 19037 Z= 0.399 Chirality : 0.051 1.410 2154 Planarity : 0.004 0.045 1395 Dihedral : 29.313 174.165 4232 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.75 % Allowed : 7.93 % Favored : 91.32 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.29), residues: 787 helix: 2.79 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -1.09 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 80 TYR 0.014 0.001 TYR A 100 PHE 0.007 0.001 PHE E 79 HIS 0.004 0.001 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.19 (13184) covalent geometry : angle 0.62037 / 0.40 (19037) hydrogen bonds : bond 0.06107 / 6.67 ( 740) hydrogen bonds : angle 2.88940 / 3.62 ( 1857) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.7710 (tttp) cc_final: 0.7270 (tttt) REVERT: A 132 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7581 (mtt-85) REVERT: B 93 ARG cc_start: 0.7690 (mtp-110) cc_final: 0.7290 (ttp80) REVERT: C 74 ASN cc_start: 0.7238 (t160) cc_final: 0.6842 (t0) REVERT: E 77 GLN cc_start: 0.6958 (tm-30) cc_final: 0.6504 (tm-30) REVERT: G 36 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7374 (mtm-85) REVERT: G 74 ASN cc_start: 0.5690 (m110) cc_final: 0.5445 (m-40) outliers start: 5 outliers final: 3 residues processed: 67 average time/residue: 0.4342 time to fit residues: 36.3100 Evaluate side-chains 70 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 36 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [10, 29, 12, 27, 84, 31, 24, 57, 99, 8, 96] chunk 10 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 57 optimal weight: 0.4980 chunk 99 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 96 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.162652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.118530 restraints weight = 49615.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.124232 restraints weight = 20051.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.127733 restraints weight = 12584.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.129523 restraints weight = 10044.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.130658 restraints weight = 9026.900| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13184 Z= 0.162 Angle : 0.597 10.902 19037 Z= 0.389 Chirality : 0.050 1.414 2154 Planarity : 0.004 0.043 1395 Dihedral : 29.323 174.460 4232 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.05 % Allowed : 8.23 % Favored : 90.72 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.60 (0.30), residues: 787 helix: 2.91 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -1.09 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 73 TYR 0.012 0.001 TYR A 100 PHE 0.004 0.001 PHE D 63 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.16 (13184) covalent geometry : angle 0.59724 / 0.39 (19037) hydrogen bonds : bond 0.05800 / 6.33 ( 740) hydrogen bonds : angle 2.81611 / 3.53 ( 1857) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.7380 (tttp) cc_final: 0.7148 (tttt) REVERT: A 132 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7588 (mtt-85) REVERT: B 93 ARG cc_start: 0.7640 (mtp-110) cc_final: 0.7240 (ttp80) REVERT: C 74 ASN cc_start: 0.7237 (t160) cc_final: 0.6803 (t0) REVERT: E 77 GLN cc_start: 0.7005 (tm-30) cc_final: 0.6553 (tm-30) REVERT: G 74 ASN cc_start: 0.5714 (m110) cc_final: 0.5457 (m-40) outliers start: 7 outliers final: 4 residues processed: 68 average time/residue: 0.3971 time to fit residues: 33.9860 Evaluate side-chains 70 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 93 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [80, 50, 96, 61, 37, 13, 91, 19, 49, 10, 39] chunk 80 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 39 optimal weight: 0.0980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 28 GLN C 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.162054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.117597 restraints weight = 51418.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.123330 restraints weight = 20464.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.126881 restraints weight = 12754.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.128844 restraints weight = 10121.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.129758 restraints weight = 9019.173| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3748 r_free = 0.3748 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3748 r_free = 0.3748 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13184 Z= 0.174 Angle : 0.602 10.872 19037 Z= 0.389 Chirality : 0.050 1.413 2154 Planarity : 0.004 0.043 1395 Dihedral : 29.334 174.136 4232 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.75 % Allowed : 8.23 % Favored : 91.02 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.30), residues: 787 helix: 2.96 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -1.08 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 73 TYR 0.012 0.001 TYR A 100 PHE 0.004 0.001 PHE D 63 HIS 0.005 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.17 (13184) covalent geometry : angle 0.60174 / 0.39 (19037) hydrogen bonds : bond 0.05760 / 6.29 ( 740) hydrogen bonds : angle 2.78963 / 3.50 ( 1857) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7627 (mtt-85) REVERT: B 93 ARG cc_start: 0.7650 (mtp-110) cc_final: 0.7233 (ttp80) REVERT: E 77 GLN cc_start: 0.7028 (tm-30) cc_final: 0.6572 (tm-30) REVERT: G 74 ASN cc_start: 0.5688 (m110) cc_final: 0.5447 (m-40) outliers start: 5 outliers final: 4 residues processed: 67 average time/residue: 0.4223 time to fit residues: 35.4374 Evaluate side-chains 70 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 83 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [49, 29, 25, 75, 44, 5, 7, 78, 90, 40, 14] chunk 49 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 40 optimal weight: 0.0980 chunk 14 optimal weight: 10.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.160216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.115563 restraints weight = 49921.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.121125 restraints weight = 20351.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.124610 restraints weight = 12880.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.126375 restraints weight = 10283.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.127463 restraints weight = 9263.492| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13184 Z= 0.204 Angle : 0.622 10.940 19037 Z= 0.398 Chirality : 0.051 1.422 2154 Planarity : 0.004 0.044 1395 Dihedral : 29.378 174.378 4232 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.90 % Allowed : 8.08 % Favored : 91.02 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.29), residues: 787 helix: 2.75 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -1.23 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 53 TYR 0.016 0.002 TYR A 100 PHE 0.008 0.001 PHE E 79 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.20 (13184) covalent geometry : angle 0.62249 / 0.40 (19037) hydrogen bonds : bond 0.06050 / 6.57 ( 740) hydrogen bonds : angle 2.89599 / 3.62 ( 1857) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7667 (mtt-85) REVERT: B 93 ARG cc_start: 0.7708 (mtp-110) cc_final: 0.7245 (ttp80) REVERT: E 77 GLN cc_start: 0.7075 (tm-30) cc_final: 0.6750 (tm-30) REVERT: G 74 ASN cc_start: 0.5700 (m110) cc_final: 0.5459 (m-40) REVERT: H 121 LYS cc_start: 0.7578 (tptm) cc_final: 0.7271 (ttmt) outliers start: 6 outliers final: 4 residues processed: 68 average time/residue: 0.3678 time to fit residues: 31.5536 Evaluate side-chains 70 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 83 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [53, 15, 27, 59, 79, 85, 55, 19, 21, 9, 98] chunk 53 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.161493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.117234 restraints weight = 48461.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.122803 restraints weight = 19884.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.126279 restraints weight = 12643.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.128174 restraints weight = 10101.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.129206 restraints weight = 9042.215| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13184 Z= 0.165 Angle : 0.596 10.899 19037 Z= 0.386 Chirality : 0.050 1.416 2154 Planarity : 0.004 0.050 1395 Dihedral : 29.374 174.425 4232 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.81 % Favored : 96.06 % Rotamer: Outliers : 0.90 % Allowed : 8.23 % Favored : 90.87 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.30), residues: 787 helix: 2.87 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -1.16 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 93 TYR 0.019 0.001 TYR D 81 PHE 0.005 0.001 PHE E 79 HIS 0.003 0.001 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.17 (13184) covalent geometry : angle 0.59584 / 0.39 (19037) hydrogen bonds : bond 0.05737 / 6.25 ( 740) hydrogen bonds : angle 2.83485 / 3.55 ( 1857) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3759.23 seconds wall clock time: 64 minutes 29.22 seconds (3869.22 seconds total)