Starting phenix.real_space_refine on Fri Aug 7 09:13:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vlr_43342/08_2026/8vlr_43342.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vlr_43342/08_2026/8vlr_43342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vlr_43342/08_2026/8vlr_43342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vlr_43342/08_2026/8vlr_43342.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vlr_43342/08_2026/8vlr_43342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vlr_43342/08_2026/8vlr_43342.map" } resolution = 2.6 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= 0.110 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 271 5.49 5 S 14 5.16 5 C 6495 2.51 5 N 2173 2.21 5 O 2704 1.98 5 H 9524 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21181 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1652 Classifications: {'peptide': 98} Modifications used: {'NH2': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1398 Classifications: {'peptide': 84} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1735 Classifications: {'peptide': 108} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1482 Classifications: {'peptide': 93} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1652 Classifications: {'peptide': 98} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1398 Classifications: {'peptide': 84} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "G" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1735 Classifications: {'peptide': 108} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1482 Classifications: {'peptide': 93} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "K" Number of atoms: 4320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 4320 Classifications: {'DNA': 136} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 135} Chain: "L" Number of atoms: 4327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 4327 Classifications: {'DNA': 136} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 135} Time building chain proxies: 3.02, per 1000 atoms: 0.14 Number of scatterers: 21181 At special positions: 0 Unit cell: (75.828, 117.48, 124.956, 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 271 15.00 O 2704 8.00 N 2173 7.00 C 6495 6.00 H 9524 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: 2.28 Conformation dependent library (CDL) restraints added in 342.5 milliseconds 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1436 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 72.5% alpha, 2.9% beta 129 base pairs and 253 stacking pairs defined. Time for finding SS restraints: 3.76 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 74 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.756A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.572A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.170A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 125 removed outlier: 3.571A pdb=" N SER D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 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 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.581A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.245A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing 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 83 through 84 removed outlier: 6.827A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.107A pdb=" N ARG C 42 " --> pdb=" O ILE D 90 " (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 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.807A 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 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.957A pdb=" N ARG G 42 " --> 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 77 through 78 416 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 314 hydrogen bonds 628 hydrogen bond angles 0 basepair planarities 129 basepair parallelities 253 stacking parallelities Total time for adding SS restraints: 4.13 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9520 1.03 - 1.23: 198 1.23 - 1.42: 5477 1.42 - 1.62: 6720 1.62 - 1.81: 24 Bond restraints: 21939 Sorted by residual: bond pdb=" C3' DT L 216 " pdb=" O3' DT L 216 " ideal model delta sigma weight residual 1.435 1.384 0.051 1.30e-02 5.92e+03 1.54e+01 bond pdb=" C3' DC K 60 " pdb=" O3' DC K 60 " ideal model delta sigma weight residual 1.435 1.385 0.050 1.30e-02 5.92e+03 1.48e+01 bond pdb=" C3' DA L 175 " pdb=" O3' DA L 175 " ideal model delta sigma weight residual 1.435 1.385 0.050 1.30e-02 5.92e+03 1.46e+01 bond pdb=" C3' DG K 81 " pdb=" O3' DG K 81 " ideal model delta sigma weight residual 1.435 1.385 0.050 1.30e-02 5.92e+03 1.46e+01 bond pdb=" C3' DC L 253 " pdb=" C2' DC L 253 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.33e+01 ... (remaining 21934 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 38095 1.87 - 3.75: 1640 3.75 - 5.62: 62 5.62 - 7.49: 2 7.49 - 9.36: 1 Bond angle restraints: 39800 Sorted by residual: angle pdb=" C LYS A 79 " pdb=" N THR A 80 " pdb=" CA THR A 80 " ideal model delta sigma weight residual 121.70 131.06 -9.36 1.80e+00 3.09e-01 2.71e+01 angle pdb=" O4' DT K 80 " pdb=" C1' DT K 80 " pdb=" N1 DT K 80 " ideal model delta sigma weight residual 108.00 111.59 -3.59 7.00e-01 2.04e+00 2.63e+01 angle pdb=" N3 DT K 90 " pdb=" C4 DT K 90 " pdb=" O4 DT K 90 " ideal model delta sigma weight residual 119.90 122.73 -2.83 6.00e-01 2.78e+00 2.23e+01 angle pdb=" N3 DT L 264 " pdb=" C4 DT L 264 " pdb=" O4 DT L 264 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.08e+01 angle pdb=" N3 DT K 80 " pdb=" C4 DT K 80 " pdb=" O4 DT K 80 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 ... (remaining 39795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.54: 7668 34.54 - 69.09: 1554 69.09 - 103.63: 14 103.63 - 138.17: 1 138.17 - 172.71: 10 Dihedral angle restraints: 9247 sinusoidal: 6765 harmonic: 2482 Sorted by residual: dihedral pdb=" C4' DC K 89 " pdb=" C3' DC K 89 " pdb=" O3' DC K 89 " pdb=" P DT K 90 " ideal model delta sinusoidal sigma weight residual -140.00 32.71 -172.71 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG L 209 " pdb=" C3' DG L 209 " pdb=" O3' DG L 209 " pdb=" P DT L 210 " ideal model delta sinusoidal sigma weight residual 220.00 51.14 168.86 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DT K 128 " pdb=" C3' DT K 128 " pdb=" O3' DT K 128 " pdb=" P DC K 129 " ideal model delta sinusoidal sigma weight residual 220.00 52.64 167.36 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 9244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1333 0.044 - 0.089: 369 0.089 - 0.133: 142 0.133 - 0.178: 167 0.178 - 0.222: 32 Chirality restraints: 2043 Sorted by residual: chirality pdb=" C3' DG K 81 " pdb=" C4' DG K 81 " pdb=" O3' DG K 81 " pdb=" C2' DG K 81 " both_signs ideal model delta sigma weight residual False -2.73 -2.51 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C3' DT K 48 " pdb=" C4' DT K 48 " pdb=" O3' DT K 48 " pdb=" C2' DT K 48 " both_signs ideal model delta sigma weight residual False -2.73 -2.51 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C3' DG L 177 " pdb=" C4' DG L 177 " pdb=" O3' DG L 177 " pdb=" C2' DG L 177 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 2040 not shown) Planarity restraints: 2251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT K 130 " -0.024 2.00e-02 2.50e+03 1.06e-02 3.35e+00 pdb=" N1 DT K 130 " 0.026 2.00e-02 2.50e+03 pdb=" C2 DT K 130 " 0.004 2.00e-02 2.50e+03 pdb=" O2 DT K 130 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DT K 130 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DT K 130 " -0.003 2.00e-02 2.50e+03 pdb=" O4 DT K 130 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DT K 130 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT K 130 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DT K 130 " 0.003 2.00e-02 2.50e+03 pdb=" H3 DT K 130 " -0.001 2.00e-02 2.50e+03 pdb=" H6 DT K 130 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA L 248 " 0.022 2.00e-02 2.50e+03 9.80e-03 3.12e+00 pdb=" N9 DA L 248 " -0.023 2.00e-02 2.50e+03 pdb=" C8 DA L 248 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DA L 248 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA L 248 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA L 248 " 0.007 2.00e-02 2.50e+03 pdb=" N6 DA L 248 " 0.002 2.00e-02 2.50e+03 pdb=" N1 DA L 248 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DA L 248 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DA L 248 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DA L 248 " -0.002 2.00e-02 2.50e+03 pdb=" H8 DA L 248 " -0.001 2.00e-02 2.50e+03 pdb=" H2 DA L 248 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA K 29 " 0.023 2.00e-02 2.50e+03 9.69e-03 3.05e+00 pdb=" N9 DA K 29 " -0.024 2.00e-02 2.50e+03 pdb=" C8 DA K 29 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DA K 29 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA K 29 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DA K 29 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA K 29 " 0.003 2.00e-02 2.50e+03 pdb=" N1 DA K 29 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA K 29 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA K 29 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DA K 29 " -0.004 2.00e-02 2.50e+03 pdb=" H8 DA K 29 " -0.001 2.00e-02 2.50e+03 pdb=" H2 DA K 29 " -0.002 2.00e-02 2.50e+03 ... (remaining 2248 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 2138 2.23 - 2.82: 40749 2.82 - 3.42: 54569 3.42 - 4.01: 83443 4.01 - 4.60: 122282 Nonbonded interactions: 303181 Sorted by model distance: nonbonded pdb="HH21 ARG B 19 " pdb=" OP2 DA K 51 " model vdw 1.641 2.450 nonbonded pdb=" O ILE F 50 " pdb=" HG1 THR F 54 " model vdw 1.645 2.450 nonbonded pdb="HH11 ARG C 11 " pdb=" O ALA C 12 " model vdw 1.656 2.450 nonbonded pdb=" OD2 ASP E 106 " pdb=" HE ARG E 131 " model vdw 1.658 2.450 nonbonded pdb=" O TYR C 39 " pdb=" HG SER D 79 " model vdw 1.666 2.450 ... (remaining 303176 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'K' and ((resid 10 and (name O5' or name C5' or name C4' or name O4' or n \ ame C3' or name O3' or name C2' or name C1' or name N1 or name C2 or name O2 or \ name N3 or name C4 or name O4 or name C5 or name C7 or name C6 or name H5' or na \ me H5'' or name H4' or name H3' or name H2' or name H2'' or name H1' or name H3 \ or name H71 or name H72 or name H73 or name H6 )) or resid 11 through 12 or resi \ d 14 through 17 or resid 19 through 23 or resid 25 through 38 or resid 40 or res \ id 42 through 51 or resid 53 through 94 or resid 96 through 105 or resid 107 or \ resid 109 through 122 or resid 124 through 127 or resid 129 or resid 131 through \ 132 or resid 138 through 139 or resid 142 or resid 144 through 145)) selection = (chain 'L' and ((resid 148 and (name O5' or name C5' or name C4' or name O4' or \ name C3' or name O3' or name C2' or name C1' or name N1 or name C2 or name O2 or \ name N3 or name C4 or name O4 or name C5 or name C7 or name C6 or name H5' or n \ ame H5'' or name H4' or name H3' or name H2' or name H2'' or name H1' or name H3 \ or name H71 or name H72 or name H73 or name H6 )) or resid 149 or resid 151 or \ resid 154 through 155 or resid 161 through 162 or resid 164 or resid 166 through \ 169 or resid 171 through 184 or resid 186 or resid 188 through 197 or resid 199 \ through 240 or resid 242 through 251 or resid 253 or resid 255 through 268 or r \ esid 270 through 274 or resid 276 through 279 or resid 281 through 283)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.990 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: 0.100 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.520 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:5.200 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: 0.7196 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 : 0.008 0.051 12415 Z= 0.661 Angle : 0.870 9.363 17924 Z= 0.729 Chirality : 0.066 0.222 2043 Planarity : 0.006 0.038 1322 Dihedral : 28.389 172.713 5431 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.40 % Allowed : 12.31 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 1.33 (0.29), residues: 750 helix: 1.49 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.65 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 71 TYR 0.017 0.002 TYR C 57 PHE 0.010 0.002 PHE E 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00801 / 0.66 (12415) covalent geometry : angle 0.86969 / 0.73 (17924) hydrogen bonds : bond 0.11013 / 7.35 ( 730) hydrogen bonds : angle 4.29346 / 3.13 ( 1852) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: C 64 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7617 (tm-30) REVERT: D 117 LYS cc_start: 0.8276 (ttpt) cc_final: 0.8018 (ttpp) REVERT: G 95 LYS cc_start: 0.8332 (tmtt) cc_final: 0.7586 (ttpt) REVERT: H 69 ASP cc_start: 0.8953 (t0) cc_final: 0.8682 (t0) outliers start: 9 outliers final: 5 residues processed: 93 average time/residue: 1.3990 time to fit residues: 138.4346 Evaluate side-chains 90 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 57 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.170874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.128044 restraints weight = 23833.875| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 0.85 r_work: 0.3333 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.0526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12415 Z= 0.177 Angle : 0.720 6.987 17924 Z= 0.440 Chirality : 0.047 0.327 2043 Planarity : 0.005 0.063 1322 Dihedral : 31.213 169.897 3917 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.18 % Allowed : 11.37 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 1.78 (0.29), residues: 750 helix: 1.84 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -0.48 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 72 TYR 0.014 0.002 TYR B 51 PHE 0.011 0.001 PHE E 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.18 (12415) covalent geometry : angle 0.71962 / 0.44 (17924) hydrogen bonds : bond 0.05351 / 3.62 ( 730) hydrogen bonds : angle 3.58229 / 2.68 ( 1852) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: C 64 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7220 (tp30) REVERT: G 64 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: G 95 LYS cc_start: 0.8224 (tmtt) cc_final: 0.7444 (ttpt) REVERT: H 69 ASP cc_start: 0.8679 (t0) cc_final: 0.8402 (t0) outliers start: 14 outliers final: 6 residues processed: 98 average time/residue: 1.6296 time to fit residues: 169.6222 Evaluate side-chains 95 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.169909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.126810 restraints weight = 23826.296| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 0.85 r_work: 0.3320 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.0647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12415 Z= 0.207 Angle : 0.713 7.488 17924 Z= 0.433 Chirality : 0.046 0.313 2043 Planarity : 0.005 0.038 1322 Dihedral : 31.291 169.831 3913 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.56 % Allowed : 11.99 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 1.81 (0.30), residues: 750 helix: 1.85 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.48 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 72 TYR 0.013 0.002 TYR C 57 PHE 0.011 0.002 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.21 (12415) covalent geometry : angle 0.71345 / 0.43 (17924) hydrogen bonds : bond 0.05516 / 3.72 ( 730) hydrogen bonds : angle 3.48100 / 2.60 ( 1852) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 64 LYS cc_start: 0.8315 (mtpt) cc_final: 0.8103 (mtmp) REVERT: G 64 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7254 (tm-30) REVERT: G 95 LYS cc_start: 0.8230 (tmtt) cc_final: 0.7456 (ttpt) outliers start: 10 outliers final: 6 residues processed: 98 average time/residue: 1.6174 time to fit residues: 168.5579 Evaluate side-chains 93 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 64 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 39 optimal weight: 0.3980 chunk 72 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.170732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.127608 restraints weight = 23855.463| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 0.85 r_work: 0.3332 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12415 Z= 0.183 Angle : 0.702 7.359 17924 Z= 0.427 Chirality : 0.045 0.314 2043 Planarity : 0.005 0.039 1322 Dihedral : 31.291 169.574 3913 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.56 % Allowed : 12.62 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 1.92 (0.30), residues: 750 helix: 1.92 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.43 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 71 TYR 0.013 0.002 TYR D 41 PHE 0.011 0.002 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.18 (12415) covalent geometry : angle 0.70240 / 0.43 (17924) hydrogen bonds : bond 0.05165 / 3.49 ( 730) hydrogen bonds : angle 3.44476 / 2.57 ( 1852) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 64 LYS cc_start: 0.8305 (mtpt) cc_final: 0.8096 (mtmp) REVERT: G 64 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7237 (tm-30) REVERT: G 95 LYS cc_start: 0.8246 (tmtt) cc_final: 0.7479 (ttpt) outliers start: 10 outliers final: 7 residues processed: 95 average time/residue: 1.4952 time to fit residues: 151.2132 Evaluate side-chains 94 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 64 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 60 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.170889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.127808 restraints weight = 23640.292| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 0.85 r_work: 0.3334 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12415 Z= 0.187 Angle : 0.695 7.521 17924 Z= 0.423 Chirality : 0.045 0.315 2043 Planarity : 0.005 0.039 1322 Dihedral : 31.308 169.494 3913 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.71 % Allowed : 12.46 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 1.97 (0.30), residues: 750 helix: 1.97 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.44 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 71 TYR 0.012 0.002 TYR A 54 PHE 0.011 0.002 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.19 (12415) covalent geometry : angle 0.69546 / 0.42 (17924) hydrogen bonds : bond 0.05098 / 3.44 ( 730) hydrogen bonds : angle 3.41115 / 2.55 ( 1852) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7160 (tp30) REVERT: E 64 LYS cc_start: 0.8256 (mtpt) cc_final: 0.8046 (mtmp) REVERT: G 64 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7149 (tm-30) REVERT: G 95 LYS cc_start: 0.8176 (tmtt) cc_final: 0.7385 (ttpt) outliers start: 11 outliers final: 6 residues processed: 96 average time/residue: 1.5041 time to fit residues: 153.6935 Evaluate side-chains 93 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.171233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.128173 restraints weight = 23707.474| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 0.85 r_work: 0.3319 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.0780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12415 Z= 0.172 Angle : 0.692 7.346 17924 Z= 0.421 Chirality : 0.045 0.314 2043 Planarity : 0.005 0.039 1322 Dihedral : 31.302 169.272 3913 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.40 % Allowed : 13.08 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 2.01 (0.30), residues: 750 helix: 2.00 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.42 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 71 TYR 0.012 0.002 TYR D 41 PHE 0.011 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.17 (12415) covalent geometry : angle 0.69161 / 0.42 (17924) hydrogen bonds : bond 0.04997 / 3.38 ( 730) hydrogen bonds : angle 3.39389 / 2.53 ( 1852) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7200 (tp30) REVERT: E 64 LYS cc_start: 0.8275 (mtpt) cc_final: 0.8069 (mtmp) REVERT: G 64 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7182 (tm-30) REVERT: G 95 LYS cc_start: 0.8216 (tmtt) cc_final: 0.7445 (ttpt) outliers start: 9 outliers final: 7 residues processed: 92 average time/residue: 1.5671 time to fit residues: 153.5224 Evaluate side-chains 94 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 64 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 50 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 85 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.171367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.128295 restraints weight = 23743.343| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 0.85 r_work: 0.3323 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12415 Z= 0.175 Angle : 0.689 7.311 17924 Z= 0.420 Chirality : 0.044 0.313 2043 Planarity : 0.004 0.039 1322 Dihedral : 31.305 169.281 3913 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.25 % Allowed : 13.08 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 2.05 (0.30), residues: 750 helix: 2.02 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.40 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 71 TYR 0.011 0.002 TYR D 41 PHE 0.011 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.17 (12415) covalent geometry : angle 0.68856 / 0.42 (17924) hydrogen bonds : bond 0.04961 / 3.35 ( 730) hydrogen bonds : angle 3.38224 / 2.52 ( 1852) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7205 (tp30) REVERT: G 64 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7187 (tm-30) REVERT: G 95 LYS cc_start: 0.8220 (tmtt) cc_final: 0.7447 (ttpt) outliers start: 8 outliers final: 6 residues processed: 91 average time/residue: 1.6249 time to fit residues: 157.4016 Evaluate side-chains 93 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 64 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 36 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 72 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.170582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.127352 restraints weight = 23776.240| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 0.85 r_work: 0.3312 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12415 Z= 0.195 Angle : 0.695 7.389 17924 Z= 0.420 Chirality : 0.045 0.315 2043 Planarity : 0.005 0.040 1322 Dihedral : 31.339 169.296 3911 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.56 % Allowed : 12.62 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 1.97 (0.30), residues: 750 helix: 1.97 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.44 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 71 TYR 0.012 0.002 TYR D 41 PHE 0.012 0.002 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.19 (12415) covalent geometry : angle 0.69543 / 0.42 (17924) hydrogen bonds : bond 0.05216 / 3.52 ( 730) hydrogen bonds : angle 3.37159 / 2.51 ( 1852) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 93 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7592 (mp10) REVERT: C 64 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7232 (tp30) REVERT: G 64 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7227 (tm-30) REVERT: G 95 LYS cc_start: 0.8255 (tmtt) cc_final: 0.7512 (ttpt) outliers start: 10 outliers final: 5 residues processed: 95 average time/residue: 1.6274 time to fit residues: 164.4387 Evaluate side-chains 92 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 9 optimal weight: 0.8980 chunk 56 optimal weight: 0.0970 chunk 32 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 70 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.172029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.128872 restraints weight = 23741.296| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 0.86 r_work: 0.3347 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12415 Z= 0.152 Angle : 0.679 6.989 17924 Z= 0.415 Chirality : 0.044 0.307 2043 Planarity : 0.005 0.039 1322 Dihedral : 31.321 169.209 3911 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.71 % Allowed : 12.62 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 2.16 (0.30), residues: 750 helix: 2.12 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.38 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 71 TYR 0.013 0.001 TYR D 41 PHE 0.011 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.15 (12415) covalent geometry : angle 0.67940 / 0.42 (17924) hydrogen bonds : bond 0.04814 / 3.26 ( 730) hydrogen bonds : angle 3.32541 / 2.48 ( 1852) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7113 (tp30) REVERT: G 64 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7126 (tm-30) REVERT: G 95 LYS cc_start: 0.8206 (tmtt) cc_final: 0.7436 (ttpt) outliers start: 11 outliers final: 6 residues processed: 94 average time/residue: 1.6072 time to fit residues: 160.5869 Evaluate side-chains 96 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.171929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.128800 restraints weight = 23718.335| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 0.85 r_work: 0.3330 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12415 Z= 0.164 Angle : 0.678 7.119 17924 Z= 0.413 Chirality : 0.044 0.309 2043 Planarity : 0.005 0.039 1322 Dihedral : 31.332 169.107 3911 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.40 % Allowed : 13.08 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 2.18 (0.30), residues: 750 helix: 2.13 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.36 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 71 TYR 0.013 0.002 TYR D 41 PHE 0.011 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.16 (12415) covalent geometry : angle 0.67776 / 0.41 (17924) hydrogen bonds : bond 0.04806 / 3.25 ( 730) hydrogen bonds : angle 3.32305 / 2.48 ( 1852) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7211 (tp30) REVERT: G 64 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7178 (tm-30) REVERT: G 95 LYS cc_start: 0.8248 (tmtt) cc_final: 0.7499 (ttpt) outliers start: 9 outliers final: 7 residues processed: 94 average time/residue: 1.5191 time to fit residues: 151.4257 Evaluate side-chains 97 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 64 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 56 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 9 optimal weight: 0.1980 chunk 64 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.171991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.128823 restraints weight = 23702.186| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 0.85 r_work: 0.3331 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12415 Z= 0.164 Angle : 0.677 7.138 17924 Z= 0.413 Chirality : 0.044 0.309 2043 Planarity : 0.005 0.039 1322 Dihedral : 31.333 169.070 3911 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.40 % Allowed : 13.24 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 2.20 (0.30), residues: 750 helix: 2.13 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.35 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 71 TYR 0.012 0.002 TYR D 41 PHE 0.010 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.16 (12415) covalent geometry : angle 0.67665 / 0.41 (17924) hydrogen bonds : bond 0.04785 / 3.24 ( 730) hydrogen bonds : angle 3.31759 / 2.48 ( 1852) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6977.62 seconds wall clock time: 118 minutes 34.12 seconds (7114.12 seconds total)