Starting phenix.real_space_refine on Wed Jun 18 03:44:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vlr_43342/06_2025/8vlr_43342.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vlr_43342/06_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_43342/06_2025/8vlr_43342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vlr_43342/06_2025/8vlr_43342.map" model { file = "/net/cci-nas-00/data/ceres_data/8vlr_43342/06_2025/8vlr_43342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vlr_43342/06_2025/8vlr_43342.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.110 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.42, per 1000 atoms: 0.54 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: 9.55 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 15.63 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: 11.88 Time building geometry restraints manager: 10.35 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: 232.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.440 Extract box with map and model: 0.870 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 70.360 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:19.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 324.550 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (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 HIS 0.005 0.001 HIS F 75 PHE 0.010 0.002 PHE E 67 TYR 0.017 0.002 TYR C 57 ARG 0.006 0.001 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.11013 ( 730) hydrogen bonds : angle 4.29346 ( 1852) covalent geometry : bond 0.00677 (12415) covalent geometry : angle 0.71669 (17924) *********************** 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 : 1.416 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: 4.3809 time to fit residues: 435.6211 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 : 1.271 ------------------------------------------------------------------------------- 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 82 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.170425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.127549 restraints weight = 23684.087| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 0.90 r_work: 0.3330 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.0596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12415 Z= 0.227 Angle : 0.659 5.930 17924 Z= 0.406 Chirality : 0.043 0.131 2043 Planarity : 0.005 0.040 1322 Dihedral : 31.072 174.171 3917 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.87 % Allowed : 11.53 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.29), residues: 750 helix: 1.83 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.47 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.009 0.002 PHE A 67 TYR 0.013 0.002 TYR C 57 ARG 0.005 0.000 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.04902 ( 730) hydrogen bonds : angle 3.43058 ( 1852) covalent geometry : bond 0.00511 (12415) covalent geometry : angle 0.65874 (17924) *********************** 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: 12 poor density : 90 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 64 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7213 (tm-30) REVERT: G 95 LYS cc_start: 0.8229 (tmtt) cc_final: 0.7453 (ttpt) outliers start: 12 outliers final: 6 residues processed: 99 average time/residue: 3.5515 time to fit residues: 373.1629 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 : 1.348 ------------------------------------------------------------------------------- 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 60 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.170249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.127313 restraints weight = 23500.093| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 0.90 r_work: 0.3324 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12415 Z= 0.234 Angle : 0.656 5.690 17924 Z= 0.402 Chirality : 0.044 0.131 2043 Planarity : 0.005 0.043 1322 Dihedral : 30.998 173.994 3913 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.87 % Allowed : 11.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.30), residues: 750 helix: 1.90 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -0.47 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.012 0.002 PHE E 67 TYR 0.013 0.002 TYR D 41 ARG 0.005 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04864 ( 730) hydrogen bonds : angle 3.33471 ( 1852) covalent geometry : bond 0.00528 (12415) covalent geometry : angle 0.65555 (17924) *********************** 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 103 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8437 (mttt) cc_final: 0.8164 (mttt) REVERT: B 93 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7594 (mp10) REVERT: E 80 THR cc_start: 0.8978 (m) cc_final: 0.8741 (p) REVERT: F 91 LYS cc_start: 0.7919 (ttpt) cc_final: 0.7661 (ttpt) REVERT: G 64 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7216 (tm-30) REVERT: G 95 LYS cc_start: 0.8217 (tmtt) cc_final: 0.7456 (ttpt) outliers start: 12 outliers final: 6 residues processed: 99 average time/residue: 3.6344 time to fit residues: 381.1854 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 : 1.385 ------------------------------------------------------------------------------- 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 E residue 115 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 61 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.169050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.126074 restraints weight = 23818.426| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 0.92 r_work: 0.3308 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12415 Z= 0.258 Angle : 0.666 5.460 17924 Z= 0.408 Chirality : 0.045 0.135 2043 Planarity : 0.005 0.041 1322 Dihedral : 30.989 172.492 3913 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.71 % Allowed : 12.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.30), residues: 750 helix: 1.85 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -0.53 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 31 PHE 0.012 0.002 PHE A 67 TYR 0.013 0.002 TYR D 41 ARG 0.007 0.001 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.05094 ( 730) hydrogen bonds : angle 3.35359 ( 1852) covalent geometry : bond 0.00582 (12415) covalent geometry : angle 0.66614 (17924) *********************** 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: 11 poor density : 89 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8424 (mttt) cc_final: 0.8153 (mttt) REVERT: B 24 ASP cc_start: 0.6070 (p0) cc_final: 0.5404 (p0) REVERT: B 93 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7542 (mp10) REVERT: C 64 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7619 (tm-30) REVERT: E 80 THR cc_start: 0.8967 (m) cc_final: 0.8753 (p) REVERT: F 91 LYS cc_start: 0.7967 (ttpt) cc_final: 0.7728 (ttpt) REVERT: G 64 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7191 (tm-30) REVERT: G 95 LYS cc_start: 0.8266 (tmtt) cc_final: 0.7531 (ttpt) outliers start: 11 outliers final: 6 residues processed: 96 average time/residue: 3.5805 time to fit residues: 365.6038 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 : 1.221 ------------------------------------------------------------------------------- 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 E residue 115 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 74 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.170364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.127302 restraints weight = 23730.443| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 0.87 r_work: 0.3326 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.0953 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= 0.199 Angle : 0.649 5.535 17924 Z= 0.401 Chirality : 0.042 0.130 2043 Planarity : 0.005 0.041 1322 Dihedral : 30.983 173.373 3913 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.71 % Allowed : 12.31 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.30), residues: 750 helix: 1.99 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.47 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.011 0.001 PHE A 67 TYR 0.013 0.002 TYR D 41 ARG 0.004 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04785 ( 730) hydrogen bonds : angle 3.28787 ( 1852) covalent geometry : bond 0.00440 (12415) covalent geometry : angle 0.64872 (17924) *********************** 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 : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8377 (mttt) cc_final: 0.8095 (mttt) REVERT: B 24 ASP cc_start: 0.6095 (p0) cc_final: 0.5312 (p0) REVERT: B 93 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7524 (mp10) REVERT: E 80 THR cc_start: 0.8968 (m) cc_final: 0.8753 (p) REVERT: F 91 LYS cc_start: 0.7971 (ttpt) cc_final: 0.7735 (ttpt) REVERT: G 64 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7190 (tm-30) REVERT: G 95 LYS cc_start: 0.8272 (tmtt) cc_final: 0.7555 (ttmt) outliers start: 11 outliers final: 6 residues processed: 95 average time/residue: 3.5572 time to fit residues: 358.1108 Evaluate side-chains 97 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 1.249 ------------------------------------------------------------------------------- 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 E residue 115 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 34 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.170088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.127097 restraints weight = 23637.075| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 0.89 r_work: 0.3320 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1010 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= 0.234 Angle : 0.652 5.397 17924 Z= 0.400 Chirality : 0.044 0.133 2043 Planarity : 0.005 0.042 1322 Dihedral : 30.972 173.103 3913 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.02 % Allowed : 12.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.30), residues: 750 helix: 1.98 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.47 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.010 0.002 PHE A 67 TYR 0.012 0.002 TYR D 41 ARG 0.007 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04711 ( 730) hydrogen bonds : angle 3.28831 ( 1852) covalent geometry : bond 0.00525 (12415) covalent geometry : angle 0.65176 (17924) *********************** 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 101 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8419 (mttt) cc_final: 0.8139 (mttt) REVERT: B 24 ASP cc_start: 0.6179 (p0) cc_final: 0.5440 (p0) REVERT: B 79 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.7912 (mttm) REVERT: B 93 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7542 (mp10) REVERT: E 80 THR cc_start: 0.8958 (m) cc_final: 0.8745 (p) REVERT: F 91 LYS cc_start: 0.7967 (ttpt) cc_final: 0.7747 (ttpt) REVERT: G 13 LYS cc_start: 0.8191 (pttm) cc_final: 0.7836 (ptmt) REVERT: G 64 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7190 (tm-30) REVERT: G 95 LYS cc_start: 0.8269 (tmtt) cc_final: 0.7551 (ttmt) outliers start: 13 outliers final: 6 residues processed: 96 average time/residue: 3.6215 time to fit residues: 368.0271 Evaluate side-chains 95 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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 79 LYS 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 E residue 115 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.170342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.127372 restraints weight = 23641.545| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 0.89 r_work: 0.3326 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.1024 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= 0.216 Angle : 0.647 5.440 17924 Z= 0.399 Chirality : 0.043 0.130 2043 Planarity : 0.005 0.041 1322 Dihedral : 30.969 173.494 3913 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.56 % Allowed : 12.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.30), residues: 750 helix: 2.00 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.46 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.011 0.002 PHE A 67 TYR 0.012 0.002 TYR D 41 ARG 0.004 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04685 ( 730) hydrogen bonds : angle 3.28245 ( 1852) covalent geometry : bond 0.00487 (12415) covalent geometry : angle 0.64740 (17924) *********************** 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 98 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8398 (mttt) cc_final: 0.8114 (mttt) REVERT: B 24 ASP cc_start: 0.6194 (p0) cc_final: 0.5445 (p0) REVERT: B 79 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.7961 (mttm) REVERT: B 93 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7538 (mp10) REVERT: C 64 GLU cc_start: 0.8150 (tp30) cc_final: 0.7757 (tm-30) REVERT: E 80 THR cc_start: 0.8964 (m) cc_final: 0.8755 (p) REVERT: F 91 LYS cc_start: 0.7970 (ttpt) cc_final: 0.7758 (ttpt) REVERT: G 13 LYS cc_start: 0.8186 (pttm) cc_final: 0.7833 (ptmt) REVERT: G 64 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7190 (tm-30) REVERT: G 95 LYS cc_start: 0.8273 (tmtt) cc_final: 0.7558 (ttmt) outliers start: 10 outliers final: 6 residues processed: 94 average time/residue: 3.6294 time to fit residues: 360.6290 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 : 1.443 ------------------------------------------------------------------------------- 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 79 LYS 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 E residue 115 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 13 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 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 = 0.3925 r_free = 0.3925 target = 0.170479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.127496 restraints weight = 23650.421| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 0.89 r_work: 0.3326 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.1031 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= 0.210 Angle : 0.645 5.441 17924 Z= 0.398 Chirality : 0.042 0.130 2043 Planarity : 0.005 0.041 1322 Dihedral : 30.968 173.555 3913 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.56 % Allowed : 12.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.30), residues: 750 helix: 2.01 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.46 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.011 0.001 PHE A 67 TYR 0.012 0.002 TYR D 41 ARG 0.005 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04652 ( 730) hydrogen bonds : angle 3.27717 ( 1852) covalent geometry : bond 0.00472 (12415) covalent geometry : angle 0.64481 (17924) *********************** 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: 10 poor density : 87 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8394 (mttt) cc_final: 0.8109 (mttt) REVERT: B 24 ASP cc_start: 0.6192 (p0) cc_final: 0.5454 (p0) REVERT: B 79 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.7958 (mttm) REVERT: B 93 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7532 (mp10) REVERT: E 80 THR cc_start: 0.8962 (m) cc_final: 0.8753 (p) REVERT: F 91 LYS cc_start: 0.7965 (ttpt) cc_final: 0.7754 (ttpt) REVERT: G 13 LYS cc_start: 0.8183 (pttm) cc_final: 0.7830 (ptmt) REVERT: G 64 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7184 (tm-30) REVERT: G 95 LYS cc_start: 0.8271 (tmtt) cc_final: 0.7554 (ttmt) outliers start: 10 outliers final: 6 residues processed: 93 average time/residue: 3.7906 time to fit residues: 374.2460 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 : 1.423 ------------------------------------------------------------------------------- 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 79 LYS 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 E residue 115 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 16 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.170199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.127177 restraints weight = 23639.086| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 0.89 r_work: 0.3324 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12415 Z= 0.232 Angle : 0.649 5.478 17924 Z= 0.399 Chirality : 0.043 0.131 2043 Planarity : 0.005 0.059 1322 Dihedral : 30.936 174.053 3913 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.71 % Allowed : 12.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.30), residues: 750 helix: 1.98 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.50 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.011 0.002 PHE A 67 TYR 0.012 0.002 TYR D 41 ARG 0.010 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04803 ( 730) hydrogen bonds : angle 3.29163 ( 1852) covalent geometry : bond 0.00525 (12415) covalent geometry : angle 0.64873 (17924) *********************** 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 100 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8436 (mttt) cc_final: 0.8171 (mttt) REVERT: B 24 ASP cc_start: 0.6043 (p0) cc_final: 0.5420 (p0) REVERT: B 79 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8099 (mttm) REVERT: B 93 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7581 (mp10) REVERT: F 91 LYS cc_start: 0.7965 (ttpt) cc_final: 0.7758 (ttpt) REVERT: G 13 LYS cc_start: 0.8154 (pttm) cc_final: 0.7811 (ptmt) REVERT: G 64 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7197 (tm-30) REVERT: G 71 ARG cc_start: 0.7316 (ttp80) cc_final: 0.6874 (ttm-80) REVERT: G 95 LYS cc_start: 0.8270 (tmtt) cc_final: 0.7551 (ttmt) outliers start: 11 outliers final: 6 residues processed: 96 average time/residue: 3.6490 time to fit residues: 370.9859 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 : 1.688 ------------------------------------------------------------------------------- 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 79 LYS 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 E residue 115 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 14 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 4 optimal weight: 0.0020 chunk 12 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.170405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.127480 restraints weight = 23554.220| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 0.88 r_work: 0.3310 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.1122 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= 0.216 Angle : 0.644 5.456 17924 Z= 0.397 Chirality : 0.043 0.129 2043 Planarity : 0.005 0.054 1322 Dihedral : 30.934 174.317 3913 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.56 % Allowed : 12.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.30), residues: 750 helix: 2.00 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.49 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.011 0.002 PHE A 67 TYR 0.013 0.002 TYR D 41 ARG 0.009 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04732 ( 730) hydrogen bonds : angle 3.27813 ( 1852) covalent geometry : bond 0.00487 (12415) covalent geometry : angle 0.64415 (17924) ********************** 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 98 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8413 (mttt) cc_final: 0.8148 (mttt) REVERT: B 24 ASP cc_start: 0.6028 (p0) cc_final: 0.5413 (p0) REVERT: B 79 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8056 (mttm) REVERT: B 93 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7511 (mp10) REVERT: F 91 LYS cc_start: 0.7930 (ttpt) cc_final: 0.7725 (ttpt) REVERT: G 13 LYS cc_start: 0.8142 (pttm) cc_final: 0.7789 (ptmt) REVERT: G 64 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7159 (tm-30) REVERT: G 71 ARG cc_start: 0.7290 (ttp80) cc_final: 0.6841 (ttm-80) REVERT: G 95 LYS cc_start: 0.8247 (tmtt) cc_final: 0.7517 (ttmt) outliers start: 10 outliers final: 6 residues processed: 94 average time/residue: 3.7148 time to fit residues: 369.6817 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 : 1.258 ------------------------------------------------------------------------------- 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 79 LYS 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 E residue 115 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 48 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.170690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.127688 restraints weight = 23653.076| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 0.86 r_work: 0.3314 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.1129 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= 0.199 Angle : 0.640 5.438 17924 Z= 0.395 Chirality : 0.042 0.130 2043 Planarity : 0.005 0.052 1322 Dihedral : 30.933 174.505 3913 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.56 % Allowed : 12.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.30), residues: 750 helix: 2.03 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.48 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.011 0.001 PHE A 67 TYR 0.013 0.001 TYR D 41 ARG 0.006 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04687 ( 730) hydrogen bonds : angle 3.27122 ( 1852) covalent geometry : bond 0.00449 (12415) covalent geometry : angle 0.63963 (17924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16303.06 seconds wall clock time: 277 minutes 59.91 seconds (16679.91 seconds total)