Starting phenix.real_space_refine on Thu Sep 18 22:26:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vlr_43342/09_2025/8vlr_43342.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vlr_43342/09_2025/8vlr_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vlr_43342/09_2025/8vlr_43342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vlr_43342/09_2025/8vlr_43342.map" model { file = "/net/cci-nas-00/data/ceres_data/8vlr_43342/09_2025/8vlr_43342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vlr_43342/09_2025/8vlr_43342.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 3.78, per 1000 atoms: 0.18 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: 1.73 Conformation dependent library (CDL) restraints added in 339.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 4.01 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: 5.03 Time building geometry restraints manager: 2.34 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' DG L 209 " pdb=" O3' DG L 209 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.02e+00 bond pdb=" C3' DA K 54 " pdb=" O3' DA K 54 " ideal model delta sigma weight residual 1.422 1.464 -0.042 3.00e-02 1.11e+03 1.97e+00 bond pdb=" C3' DT K 90 " pdb=" O3' DT K 90 " ideal model delta sigma weight residual 1.422 1.464 -0.042 3.00e-02 1.11e+03 1.96e+00 bond pdb=" CA LYS A 79 " pdb=" CB LYS A 79 " ideal model delta sigma weight residual 1.524 1.542 -0.017 1.22e-02 6.72e+03 1.95e+00 bond pdb=" O5' DG L 177 " pdb=" C5' DG L 177 " ideal model delta sigma weight residual 1.423 1.381 0.042 3.00e-02 1.11e+03 1.93e+00 ... (remaining 21934 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 38508 1.87 - 3.75: 1271 3.75 - 5.62: 18 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=" CB LYS C 36 " pdb=" CG LYS C 36 " pdb=" CD LYS C 36 " ideal model delta sigma weight residual 111.30 118.78 -7.48 2.30e+00 1.89e-01 1.06e+01 angle pdb=" C3' DA K 109 " pdb=" C2' DA K 109 " pdb=" C1' DA K 109 " ideal model delta sigma weight residual 101.60 105.62 -4.02 1.50e+00 4.44e-01 7.19e+00 angle pdb=" C3' DT K 45 " pdb=" C2' DT K 45 " pdb=" C1' DT K 45 " ideal model delta sigma weight residual 101.60 105.51 -3.91 1.50e+00 4.44e-01 6.80e+00 angle pdb=" C3' DT K 86 " pdb=" C2' DT K 86 " pdb=" C1' DT K 86 " ideal model delta sigma weight residual 101.60 105.43 -3.83 1.50e+00 4.44e-01 6.52e+00 ... (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 - 0.030: 1018 0.030 - 0.061: 606 0.061 - 0.091: 279 0.091 - 0.121: 120 0.121 - 0.151: 20 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 -2.66 -2.51 -0.15 2.00e-01 2.50e+01 5.73e-01 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 -2.66 -2.51 -0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA ILE C 102 " pdb=" N ILE C 102 " pdb=" C ILE C 102 " pdb=" CB ILE C 102 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 ... (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: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 0.220 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 23.040 Find NCS groups from input model: 0.200 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:8.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 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 : 0.007 0.046 12415 Z= 0.301 Angle : 0.717 9.363 17924 Z= 0.437 Chirality : 0.048 0.151 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 aren 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 covalent geometry : bond 0.00677 (12415) covalent geometry : angle 0.71669 (17924) hydrogen bonds : bond 0.11013 ( 730) hydrogen bonds : angle 4.29346 ( 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 : 0.478 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: 1.8213 time to fit residues: 178.6356 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 : 0.401 ------------------------------------------------------------------------------- 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: 3.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3940 r_free = 0.3940 target = 0.172217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.129348 restraints weight = 23803.714| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 0.86 r_work: 0.3351 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12415 Z= 0.198 Angle : 0.646 5.950 17924 Z= 0.400 Chirality : 0.041 0.126 2043 Planarity : 0.005 0.042 1322 Dihedral : 31.052 175.944 3917 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.71 % Allowed : 11.37 % Favored : 86.92 % 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 aren not related in a simple way. whole: 1.97 (0.30), residues: 750 helix: 1.95 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.38 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 71 TYR 0.013 0.002 TYR D 41 PHE 0.009 0.001 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00443 (12415) covalent geometry : angle 0.64586 (17924) hydrogen bonds : bond 0.04499 ( 730) hydrogen bonds : angle 3.37835 ( 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 102 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7231 (tp30) REVERT: G 64 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7232 (tm-30) REVERT: G 95 LYS cc_start: 0.8235 (tmtt) cc_final: 0.7466 (ttpt) REVERT: H 69 ASP cc_start: 0.8659 (t0) cc_final: 0.8432 (t70) outliers start: 11 outliers final: 4 residues processed: 98 average time/residue: 1.8657 time to fit residues: 192.7900 Evaluate side-chains 91 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=4.50 ------------------------------------------------------------------------------- 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: 1.9990 chunk 93 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3904 r_free = 0.3904 target = 0.168424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.125434 restraints weight = 23774.381| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 0.92 r_work: 0.3304 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.0679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 12415 Z= 0.281 Angle : 0.680 5.696 17924 Z= 0.414 Chirality : 0.047 0.138 2043 Planarity : 0.006 0.044 1322 Dihedral : 31.028 172.268 3909 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.71 % Allowed : 11.84 % 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 aren not related in a simple way. whole: 1.74 (0.29), residues: 750 helix: 1.78 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -0.50 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 71 TYR 0.014 0.002 TYR C 57 PHE 0.013 0.002 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00636 (12415) covalent geometry : angle 0.68014 (17924) hydrogen bonds : bond 0.05534 ( 730) hydrogen bonds : angle 3.42933 ( 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 96 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: B 93 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7514 (mp10) REVERT: E 80 THR cc_start: 0.8974 (m) cc_final: 0.8749 (p) REVERT: F 91 LYS cc_start: 0.7906 (ttpt) cc_final: 0.7644 (ttpt) REVERT: G 64 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7198 (tm-30) REVERT: G 95 LYS cc_start: 0.8264 (tmtt) cc_final: 0.7521 (ttpt) REVERT: H 69 ASP cc_start: 0.8766 (t0) cc_final: 0.8527 (t0) outliers start: 11 outliers final: 4 residues processed: 93 average time/residue: 1.8060 time to fit residues: 177.4342 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 : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP 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: 0.2980 chunk 49 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 39 optimal weight: 0.2980 chunk 72 optimal weight: 10.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 0.0030 chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3936 r_free = 0.3936 target = 0.171698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.128755 restraints weight = 23769.420| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 0.86 r_work: 0.3341 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12415 Z= 0.179 Angle : 0.647 5.641 17924 Z= 0.401 Chirality : 0.039 0.132 2043 Planarity : 0.005 0.039 1322 Dihedral : 31.008 174.375 3909 Min Nonbonded Distance : 2.245 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 aren not related in a simple way. whole: 2.13 (0.30), residues: 750 helix: 2.11 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.43 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 71 TYR 0.013 0.001 TYR D 41 PHE 0.010 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00396 (12415) covalent geometry : angle 0.64718 (17924) hydrogen bonds : bond 0.04583 ( 730) hydrogen bonds : angle 3.31811 ( 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 100 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: B 93 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7628 (mp10) REVERT: E 80 THR cc_start: 0.8966 (m) cc_final: 0.8738 (p) REVERT: F 91 LYS cc_start: 0.7892 (ttpt) cc_final: 0.7638 (ttpt) REVERT: G 64 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7179 (tm-30) REVERT: G 95 LYS cc_start: 0.8258 (tmtt) cc_final: 0.7519 (ttpt) outliers start: 10 outliers final: 3 residues processed: 97 average time/residue: 1.8576 time to fit residues: 190.0393 Evaluate side-chains 92 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 60 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.171378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.128379 restraints weight = 23562.988| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 0.87 r_work: 0.3337 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12415 Z= 0.202 Angle : 0.642 5.483 17924 Z= 0.397 Chirality : 0.042 0.130 2043 Planarity : 0.005 0.040 1322 Dihedral : 30.991 174.603 3909 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.25 % Allowed : 12.62 % Favored : 86.14 % 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 aren not related in a simple way. whole: 2.17 (0.30), residues: 750 helix: 2.11 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.37 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 71 TYR 0.013 0.002 TYR D 41 PHE 0.010 0.001 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00449 (12415) covalent geometry : angle 0.64198 (17924) hydrogen bonds : bond 0.04456 ( 730) hydrogen bonds : angle 3.26512 ( 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 95 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: B 93 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7672 (mp10) REVERT: C 64 GLU cc_start: 0.8030 (tp30) cc_final: 0.7660 (tm-30) REVERT: E 80 THR cc_start: 0.8974 (m) cc_final: 0.8741 (p) REVERT: F 91 LYS cc_start: 0.7903 (ttpt) cc_final: 0.7670 (ttpt) REVERT: G 64 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7196 (tm-30) REVERT: G 95 LYS cc_start: 0.8265 (tmtt) cc_final: 0.7526 (ttpt) outliers start: 8 outliers final: 4 residues processed: 94 average time/residue: 1.9403 time to fit residues: 192.1292 Evaluate side-chains 91 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 20 optimal weight: 0.0980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3934 r_free = 0.3934 target = 0.171486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.128488 restraints weight = 23637.541| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 0.87 r_work: 0.3337 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12415 Z= 0.205 Angle : 0.641 5.542 17924 Z= 0.395 Chirality : 0.042 0.129 2043 Planarity : 0.005 0.039 1322 Dihedral : 30.982 174.805 3909 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.09 % Allowed : 12.77 % Favored : 86.14 % 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 aren not related in a simple way. whole: 2.21 (0.30), residues: 750 helix: 2.14 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.36 (0.41), residues: 205 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 0.011 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00462 (12415) covalent geometry : angle 0.64077 (17924) hydrogen bonds : bond 0.04441 ( 730) hydrogen bonds : angle 3.25572 ( 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 93 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: B 93 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7700 (mp10) REVERT: E 80 THR cc_start: 0.8983 (m) cc_final: 0.8754 (p) REVERT: F 91 LYS cc_start: 0.7951 (ttpt) cc_final: 0.7730 (ttpt) REVERT: G 64 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7227 (tm-30) REVERT: G 95 LYS cc_start: 0.8286 (tmtt) cc_final: 0.7561 (ttpt) outliers start: 7 outliers final: 5 residues processed: 93 average time/residue: 1.9463 time to fit residues: 190.7301 Evaluate side-chains 92 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 50 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3929 r_free = 0.3929 target = 0.171015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.128024 restraints weight = 23638.266| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 0.88 r_work: 0.3303 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12415 Z= 0.217 Angle : 0.641 5.540 17924 Z= 0.395 Chirality : 0.043 0.130 2043 Planarity : 0.005 0.041 1322 Dihedral : 30.937 175.461 3909 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.40 % Allowed : 12.46 % Favored : 86.14 % 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 aren not related in a simple way. whole: 2.15 (0.30), residues: 750 helix: 2.11 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.41 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 71 TYR 0.013 0.002 TYR D 41 PHE 0.011 0.002 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00488 (12415) covalent geometry : angle 0.64111 (17924) hydrogen bonds : bond 0.04692 ( 730) hydrogen bonds : angle 3.25123 ( 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 97 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8397 (mttt) cc_final: 0.8101 (mttt) REVERT: B 24 ASP cc_start: 0.6025 (p0) cc_final: 0.5208 (p0) REVERT: B 93 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7436 (mp10) REVERT: E 80 THR cc_start: 0.8959 (m) cc_final: 0.8741 (p) REVERT: F 91 LYS cc_start: 0.7927 (ttpt) cc_final: 0.7719 (ttpt) REVERT: G 13 LYS cc_start: 0.8180 (pttm) cc_final: 0.7821 (ptmt) REVERT: G 64 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7160 (tm-30) REVERT: G 95 LYS cc_start: 0.8252 (tmtt) cc_final: 0.7528 (ttmt) outliers start: 9 outliers final: 5 residues processed: 95 average time/residue: 1.9479 time to fit residues: 194.8482 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 : 0.480 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 72 optimal weight: 10.9990 chunk 89 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.171249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.128193 restraints weight = 23684.274| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 0.87 r_work: 0.3335 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12415 Z= 0.208 Angle : 0.638 5.520 17924 Z= 0.394 Chirality : 0.042 0.129 2043 Planarity : 0.005 0.041 1322 Dihedral : 30.937 175.656 3909 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.40 % Allowed : 12.46 % Favored : 86.14 % 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 aren not related in a simple way. whole: 2.18 (0.30), residues: 750 helix: 2.13 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.40 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 covalent geometry : bond 0.00466 (12415) covalent geometry : angle 0.63833 (17924) hydrogen bonds : bond 0.04618 ( 730) hydrogen bonds : angle 3.23631 ( 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 97 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8190 (mtm-85) cc_final: 0.7970 (mtm-85) REVERT: A 115 LYS cc_start: 0.8396 (mttt) cc_final: 0.8098 (mttt) REVERT: B 24 ASP cc_start: 0.6032 (p0) cc_final: 0.5201 (p0) REVERT: B 93 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7433 (mp10) REVERT: E 80 THR cc_start: 0.8963 (m) cc_final: 0.8742 (p) REVERT: G 13 LYS cc_start: 0.8180 (pttm) cc_final: 0.7826 (ptmt) REVERT: G 64 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7164 (tm-30) REVERT: G 95 LYS cc_start: 0.8249 (tmtt) cc_final: 0.7523 (ttmt) outliers start: 9 outliers final: 5 residues processed: 94 average time/residue: 1.9467 time to fit residues: 192.8679 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 : 0.442 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 9 optimal weight: 0.8980 chunk 56 optimal weight: 0.3980 chunk 32 optimal weight: 0.0980 chunk 60 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 64 ASN G 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.171918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.128849 restraints weight = 23637.389| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 0.86 r_work: 0.3341 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12415 Z= 0.180 Angle : 0.632 5.532 17924 Z= 0.392 Chirality : 0.040 0.132 2043 Planarity : 0.005 0.040 1322 Dihedral : 30.936 176.221 3909 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.40 % Allowed : 12.46 % Favored : 86.14 % 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 aren not related in a simple way. whole: 2.24 (0.30), residues: 750 helix: 2.17 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.38 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 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 covalent geometry : bond 0.00399 (12415) covalent geometry : angle 0.63167 (17924) hydrogen bonds : bond 0.04509 ( 730) hydrogen bonds : angle 3.22145 ( 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 97 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8200 (mtm-85) cc_final: 0.7984 (mtm-85) REVERT: A 115 LYS cc_start: 0.8380 (mttt) cc_final: 0.8072 (mttt) REVERT: B 24 ASP cc_start: 0.5981 (p0) cc_final: 0.5158 (p0) REVERT: B 93 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7432 (mp10) REVERT: E 80 THR cc_start: 0.8966 (m) cc_final: 0.8749 (p) REVERT: G 13 LYS cc_start: 0.8179 (pttm) cc_final: 0.7829 (ptmt) REVERT: G 64 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7167 (tm-30) REVERT: G 95 LYS cc_start: 0.8260 (tmtt) cc_final: 0.7541 (ttmt) outliers start: 9 outliers final: 5 residues processed: 93 average time/residue: 1.9940 time to fit residues: 195.2240 Evaluate side-chains 94 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 0.0570 chunk 85 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3934 r_free = 0.3934 target = 0.171612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.128572 restraints weight = 23615.502| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 0.87 r_work: 0.3339 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12415 Z= 0.205 Angle : 0.635 5.510 17924 Z= 0.392 Chirality : 0.041 0.129 2043 Planarity : 0.005 0.040 1322 Dihedral : 30.935 175.839 3909 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.25 % Allowed : 12.62 % Favored : 86.14 % 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 aren not related in a simple way. whole: 2.23 (0.30), residues: 750 helix: 2.16 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.37 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 71 TYR 0.012 0.002 TYR D 41 PHE 0.010 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00459 (12415) covalent geometry : angle 0.63524 (17924) hydrogen bonds : bond 0.04492 ( 730) hydrogen bonds : angle 3.22642 ( 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 96 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8177 (mtm-85) cc_final: 0.7964 (mtm-85) REVERT: A 115 LYS cc_start: 0.8370 (mttt) cc_final: 0.8063 (mttt) REVERT: B 24 ASP cc_start: 0.5958 (p0) cc_final: 0.5154 (p0) REVERT: B 93 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7429 (mp10) REVERT: C 64 GLU cc_start: 0.7972 (tp30) cc_final: 0.7665 (tm-30) REVERT: E 80 THR cc_start: 0.8960 (m) cc_final: 0.8741 (p) REVERT: G 13 LYS cc_start: 0.8174 (pttm) cc_final: 0.7820 (ptmt) REVERT: G 64 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7164 (tm-30) REVERT: G 95 LYS cc_start: 0.8246 (tmtt) cc_final: 0.7521 (ttmt) outliers start: 8 outliers final: 5 residues processed: 93 average time/residue: 1.9861 time to fit residues: 194.2374 Evaluate side-chains 94 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 56 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3937 r_free = 0.3937 target = 0.171818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.128814 restraints weight = 23605.501| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 0.85 r_work: 0.3342 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12415 Z= 0.190 Angle : 0.632 5.501 17924 Z= 0.391 Chirality : 0.041 0.130 2043 Planarity : 0.005 0.040 1322 Dihedral : 30.935 176.082 3909 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.25 % Allowed : 12.62 % Favored : 86.14 % 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 aren not related in a simple way. whole: 2.25 (0.30), residues: 750 helix: 2.18 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.37 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 71 TYR 0.012 0.001 TYR D 41 PHE 0.010 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00426 (12415) covalent geometry : angle 0.63209 (17924) hydrogen bonds : bond 0.04461 ( 730) hydrogen bonds : angle 3.22277 ( 1852) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7742.62 seconds wall clock time: 131 minutes 35.49 seconds (7895.49 seconds total)