Starting phenix.real_space_refine on Sat Aug 23 08:23:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ek1_28192/08_2025/8ek1_28192.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ek1_28192/08_2025/8ek1_28192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ek1_28192/08_2025/8ek1_28192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ek1_28192/08_2025/8ek1_28192.map" model { file = "/net/cci-nas-00/data/ceres_data/8ek1_28192/08_2025/8ek1_28192.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ek1_28192/08_2025/8ek1_28192.cif" } resolution = 3.6 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= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2884 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 5364 2.51 5 N 1438 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8497 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 934 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "B" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "C" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1607 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 197} Chain breaks: 1 Chain: "D" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1652 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "H" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1633 Classifications: {'peptide': 215} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 202} Chain breaks: 1 Chain: "L" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1652 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "P" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 195 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 6, 'TRANS': 20} Time building chain proxies: 2.20, per 1000 atoms: 0.26 Number of scatterers: 8497 At special positions: 0 Unit cell: (78.2, 126.96, 147.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1663 8.00 N 1438 7.00 C 5364 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 147 " - pdb=" SG CYS C 203 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 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: 0.86 Conformation dependent library (CDL) restraints added in 337.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 25 sheets defined 3.6% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.083A pdb=" N VAL B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 165 No H-bonds generated for 'chain 'C' and resid 163 through 165' Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 183 through 188 Processing helix chain 'H' and resid 163 through 165 No H-bonds generated for 'chain 'H' and resid 163 through 165' Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 removed outlier: 3.688A pdb=" N LEU A 20 " --> pdb=" O MET A 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 52 removed outlier: 5.745A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL A 37 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 19 through 22 removed outlier: 3.533A pdb=" N VAL B 19 " --> pdb=" O ILE B 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 45 through 48 removed outlier: 6.601A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU B 90 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR B 97 " --> pdb=" O GLU B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.981A pdb=" N SER C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ARG C 16 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET C 83 " --> pdb=" O LEU C 18 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.348A pdb=" N GLY C 10 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL C 37 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TYR C 59 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.348A pdb=" N GLY C 10 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP C 102 " --> pdb=" O GLY C 105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 127 through 130 removed outlier: 6.339A pdb=" N TYR C 183 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 127 through 130 removed outlier: 6.339A pdb=" N TYR C 183 " --> pdb=" O ASP C 151 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER C 184 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 157 through 161 Processing sheet with id=AB2, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AB3, first strand: chain 'D' and resid 45 through 49 removed outlier: 5.509A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE D 48 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU D 90 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR D 97 " --> pdb=" O GLU D 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 85 through 86 Processing sheet with id=AB5, first strand: chain 'D' and resid 114 through 118 removed outlier: 3.762A pdb=" N VAL D 133 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 145 through 150 Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.564A pdb=" N LYS H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER H 25 " --> pdb=" O LYS H 3 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER H 71 " --> pdb=" O PHE H 80 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.235A pdb=" N GLY H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR H 94 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 105 through 110 removed outlier: 9.798A pdb=" N ASP P 15 " --> pdb=" O ASN H 99 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N TYR H 101 " --> pdb=" O ASP P 15 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 127 through 131 removed outlier: 3.789A pdb=" N GLY H 146 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 127 through 131 removed outlier: 3.789A pdb=" N GLY H 146 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER H 184 " --> pdb=" O VAL H 176 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL H 176 " --> pdb=" O SER H 184 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 157 through 161 removed outlier: 3.525A pdb=" N LYS H 216 " --> pdb=" O CYS H 203 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.688A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA L 13 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.838A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 145 through 150 269 hydrogen bonds defined for protein. 681 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1488 1.32 - 1.45: 2495 1.45 - 1.58: 4680 1.58 - 1.71: 0 1.71 - 1.83: 44 Bond restraints: 8707 Sorted by residual: bond pdb=" CA ALA D 84 " pdb=" CB ALA D 84 " ideal model delta sigma weight residual 1.530 1.478 0.052 1.69e-02 3.50e+03 9.50e+00 bond pdb=" C GLU D 68 " pdb=" O GLU D 68 " ideal model delta sigma weight residual 1.235 1.198 0.038 1.26e-02 6.30e+03 8.92e+00 bond pdb=" N ASN D 210 " pdb=" CA ASN D 210 " ideal model delta sigma weight residual 1.456 1.492 -0.035 1.21e-02 6.83e+03 8.45e+00 bond pdb=" N ASP D 81 " pdb=" CA ASP D 81 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.16e-02 7.43e+03 7.97e+00 bond pdb=" C ALA D 84 " pdb=" O ALA D 84 " ideal model delta sigma weight residual 1.235 1.203 0.032 1.26e-02 6.30e+03 6.46e+00 ... (remaining 8702 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 11266 1.52 - 3.05: 442 3.05 - 4.57: 101 4.57 - 6.10: 19 6.10 - 7.62: 6 Bond angle restraints: 11834 Sorted by residual: angle pdb=" C THR D 85 " pdb=" CA THR D 85 " pdb=" CB THR D 85 " ideal model delta sigma weight residual 109.89 117.51 -7.62 1.69e+00 3.50e-01 2.03e+01 angle pdb=" N PRO D 80 " pdb=" CA PRO D 80 " pdb=" CB PRO D 80 " ideal model delta sigma weight residual 103.25 98.78 4.47 1.05e+00 9.07e-01 1.81e+01 angle pdb=" C GLN L 27 " pdb=" CA GLN L 27 " pdb=" CB GLN L 27 " ideal model delta sigma weight residual 115.89 110.93 4.96 1.32e+00 5.74e-01 1.41e+01 angle pdb=" CA GLU C 89 " pdb=" CB GLU C 89 " pdb=" CG GLU C 89 " ideal model delta sigma weight residual 114.10 121.32 -7.22 2.00e+00 2.50e-01 1.30e+01 angle pdb=" C PHE A 27 " pdb=" CA PHE A 27 " pdb=" CB PHE A 27 " ideal model delta sigma weight residual 115.89 111.17 4.72 1.32e+00 5.74e-01 1.28e+01 ... (remaining 11829 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 4487 17.48 - 34.97: 513 34.97 - 52.45: 133 52.45 - 69.94: 22 69.94 - 87.42: 8 Dihedral angle restraints: 5163 sinusoidal: 1989 harmonic: 3174 Sorted by residual: dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 88 " pdb=" CB CYS B 88 " ideal model delta sinusoidal sigma weight residual -86.00 -160.00 74.00 1 1.00e+01 1.00e-02 6.95e+01 dihedral pdb=" CB CYS L 134 " pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " pdb=" CB CYS L 194 " ideal model delta sinusoidal sigma weight residual 93.00 162.21 -69.21 1 1.00e+01 1.00e-02 6.19e+01 dihedral pdb=" CB CYS C 147 " pdb=" SG CYS C 147 " pdb=" SG CYS C 203 " pdb=" CB CYS C 203 " ideal model delta sinusoidal sigma weight residual -86.00 -143.22 57.22 1 1.00e+01 1.00e-02 4.40e+01 ... (remaining 5160 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1015 0.049 - 0.098: 204 0.098 - 0.148: 78 0.148 - 0.197: 1 0.197 - 0.246: 3 Chirality restraints: 1301 Sorted by residual: chirality pdb=" CA VAL D 83 " pdb=" N VAL D 83 " pdb=" C VAL D 83 " pdb=" CB VAL D 83 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ASP D 81 " pdb=" N ASP D 81 " pdb=" C ASP D 81 " pdb=" CB ASP D 81 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA LEU D 78 " pdb=" N LEU D 78 " pdb=" C LEU D 78 " pdb=" CB LEU D 78 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.78e-01 ... (remaining 1298 not shown) Planarity restraints: 1519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 89 " -0.012 2.00e-02 2.50e+03 2.53e-02 6.42e+00 pdb=" CD GLU C 89 " 0.044 2.00e-02 2.50e+03 pdb=" OE1 GLU C 89 " -0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU C 89 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 68 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.94e+00 pdb=" C GLU D 68 " 0.042 2.00e-02 2.50e+03 pdb=" O GLU D 68 " -0.016 2.00e-02 2.50e+03 pdb=" N THR D 69 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 67 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C SER D 67 " 0.039 2.00e-02 2.50e+03 pdb=" O SER D 67 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU D 68 " -0.013 2.00e-02 2.50e+03 ... (remaining 1516 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 551 2.73 - 3.27: 7779 3.27 - 3.81: 12178 3.81 - 4.36: 13947 4.36 - 4.90: 25616 Nonbonded interactions: 60071 Sorted by model distance: nonbonded pdb=" OD1 ASP H 102 " pdb=" N GLY H 103 " model vdw 2.185 3.120 nonbonded pdb=" NH1 ARG A 67 " pdb=" O ASP A 84 " model vdw 2.218 3.120 nonbonded pdb=" O PHE D 62 " pdb=" OG1 THR D 74 " model vdw 2.227 3.040 nonbonded pdb=" O SER H 195 " pdb=" OG1 THR H 198 " model vdw 2.230 3.040 nonbonded pdb=" O GLN D 124 " pdb=" OG SER D 127 " model vdw 2.263 3.040 ... (remaining 60066 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 'C' selection = (chain 'H' and (resid 1 through 133 or resid 144 through 220)) } ncs_group { reference = chain 'D' selection = chain 'L' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.510 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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 : 0.004 0.052 8717 Z= 0.198 Angle : 0.740 7.623 11854 Z= 0.417 Chirality : 0.046 0.246 1301 Planarity : 0.005 0.042 1519 Dihedral : 15.719 87.423 3105 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.23 % Favored : 90.31 % Rotamer: Outliers : 0.53 % Allowed : 27.19 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % 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: -1.95 (0.25), residues: 1084 helix: -0.83 (0.85), residues: 32 sheet: -0.08 (0.26), residues: 450 loop : -2.41 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 211 TYR 0.015 0.001 TYR C 152 PHE 0.018 0.001 PHE D 139 TRP 0.018 0.001 TRP L 148 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 8707) covalent geometry : angle 0.73550 (11834) SS BOND : bond 0.00432 ( 10) SS BOND : angle 2.15680 ( 20) hydrogen bonds : bond 0.18018 ( 240) hydrogen bonds : angle 7.61778 ( 681) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.8503 (mmtt) cc_final: 0.8117 (mttt) outliers start: 5 outliers final: 2 residues processed: 116 average time/residue: 0.1187 time to fit residues: 18.1319 Evaluate side-chains 111 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain D residue 209 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 0.0170 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 HIS ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.133094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.097996 restraints weight = 15246.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.098938 restraints weight = 12998.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.098824 restraints weight = 11350.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.098947 restraints weight = 11336.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.099031 restraints weight = 11335.496| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8717 Z= 0.162 Angle : 0.636 7.399 11854 Z= 0.336 Chirality : 0.044 0.153 1301 Planarity : 0.005 0.084 1519 Dihedral : 4.964 34.426 1192 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.24 % Favored : 89.67 % Rotamer: Outliers : 4.21 % Allowed : 22.87 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % 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: -1.88 (0.26), residues: 1084 helix: -0.40 (0.85), residues: 32 sheet: -0.21 (0.25), residues: 493 loop : -2.35 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 16 TYR 0.012 0.001 TYR A 95 PHE 0.011 0.001 PHE L 28 TRP 0.015 0.001 TRP D 32 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 8707) covalent geometry : angle 0.63418 (11834) SS BOND : bond 0.00622 ( 10) SS BOND : angle 1.43361 ( 20) hydrogen bonds : bond 0.04031 ( 240) hydrogen bonds : angle 6.13509 ( 681) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 LYS cc_start: 0.9236 (ttmt) cc_final: 0.8791 (mtpt) REVERT: C 151 ASP cc_start: 0.7065 (t0) cc_final: 0.6464 (t0) REVERT: C 152 TYR cc_start: 0.8745 (p90) cc_final: 0.8528 (p90) REVERT: D 79 GLN cc_start: 0.7408 (mt0) cc_final: 0.7002 (pm20) REVERT: D 151 ASP cc_start: 0.6136 (m-30) cc_final: 0.5847 (m-30) REVERT: D 210 ASN cc_start: 0.6271 (t0) cc_final: 0.5682 (p0) REVERT: H 43 LYS cc_start: 0.8560 (mmtt) cc_final: 0.7837 (mttp) outliers start: 40 outliers final: 20 residues processed: 149 average time/residue: 0.0992 time to fit residues: 20.3178 Evaluate side-chains 130 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 150 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 81 optimal weight: 0.0870 chunk 53 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS H 178 GLN L 158 ASN ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.133744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.098809 restraints weight = 15284.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.099584 restraints weight = 12695.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.099767 restraints weight = 11022.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.100130 restraints weight = 10699.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.100146 restraints weight = 10866.387| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8717 Z= 0.143 Angle : 0.619 7.324 11854 Z= 0.322 Chirality : 0.044 0.145 1301 Planarity : 0.005 0.055 1519 Dihedral : 4.737 26.634 1190 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.23 % Favored : 90.68 % Rotamer: Outliers : 4.53 % Allowed : 23.71 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % 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: -1.85 (0.25), residues: 1084 helix: -0.56 (0.82), residues: 32 sheet: -0.19 (0.25), residues: 489 loop : -2.31 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 211 TYR 0.011 0.001 TYR A 95 PHE 0.010 0.001 PHE L 28 TRP 0.014 0.001 TRP D 32 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8707) covalent geometry : angle 0.61684 (11834) SS BOND : bond 0.00601 ( 10) SS BOND : angle 1.49451 ( 20) hydrogen bonds : bond 0.03608 ( 240) hydrogen bonds : angle 5.83431 ( 681) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 113 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: C 124 LYS cc_start: 0.9204 (ttmt) cc_final: 0.8776 (mtpt) REVERT: C 151 ASP cc_start: 0.7033 (t0) cc_final: 0.6453 (t0) REVERT: D 79 GLN cc_start: 0.7351 (mt0) cc_final: 0.6750 (pm20) REVERT: D 151 ASP cc_start: 0.6175 (m-30) cc_final: 0.5913 (m-30) REVERT: D 187 GLU cc_start: 0.8553 (mm-30) cc_final: 0.7974 (mm-30) REVERT: D 210 ASN cc_start: 0.6295 (t0) cc_final: 0.5597 (p0) outliers start: 43 outliers final: 26 residues processed: 150 average time/residue: 0.0970 time to fit residues: 20.2840 Evaluate side-chains 134 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 38 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 28 optimal weight: 0.0020 chunk 73 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 GLN L 158 ASN L 189 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.133499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.098704 restraints weight = 15475.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.099388 restraints weight = 13894.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.099640 restraints weight = 12092.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099938 restraints weight = 11104.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.100023 restraints weight = 10879.521| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8717 Z= 0.136 Angle : 0.612 7.246 11854 Z= 0.317 Chirality : 0.044 0.144 1301 Planarity : 0.005 0.057 1519 Dihedral : 4.644 26.713 1190 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.50 % Favored : 90.41 % Rotamer: Outliers : 4.32 % Allowed : 23.39 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % 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: -1.85 (0.25), residues: 1084 helix: -0.58 (0.81), residues: 32 sheet: -0.21 (0.25), residues: 489 loop : -2.27 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 87 TYR 0.029 0.001 TYR C 152 PHE 0.010 0.001 PHE L 28 TRP 0.013 0.001 TRP D 32 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8707) covalent geometry : angle 0.60898 (11834) SS BOND : bond 0.00565 ( 10) SS BOND : angle 1.53966 ( 20) hydrogen bonds : bond 0.03368 ( 240) hydrogen bonds : angle 5.64352 ( 681) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 113 time to evaluate : 0.347 Fit side-chains REVERT: C 124 LYS cc_start: 0.9156 (ttmt) cc_final: 0.8731 (mtpt) REVERT: C 204 ASN cc_start: 0.8458 (p0) cc_final: 0.8225 (p0) REVERT: D 151 ASP cc_start: 0.5888 (m-30) cc_final: 0.5670 (m-30) REVERT: D 187 GLU cc_start: 0.8527 (mm-30) cc_final: 0.7945 (mm-30) REVERT: D 197 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8179 (p) REVERT: D 210 ASN cc_start: 0.6167 (t0) cc_final: 0.5571 (p0) REVERT: H 43 LYS cc_start: 0.8391 (mmtt) cc_final: 0.7738 (mttp) outliers start: 41 outliers final: 26 residues processed: 150 average time/residue: 0.0958 time to fit residues: 20.0017 Evaluate side-chains 138 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 12 optimal weight: 0.0670 chunk 106 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 67 optimal weight: 0.0870 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 overall best weight: 1.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.132667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.097443 restraints weight = 15354.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.098300 restraints weight = 13949.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.098717 restraints weight = 11689.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.098698 restraints weight = 11063.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.098811 restraints weight = 11267.570| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8717 Z= 0.161 Angle : 0.640 8.043 11854 Z= 0.332 Chirality : 0.045 0.144 1301 Planarity : 0.005 0.053 1519 Dihedral : 4.749 26.403 1190 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.15 % Favored : 89.76 % Rotamer: Outliers : 5.27 % Allowed : 23.39 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % 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: -1.84 (0.26), residues: 1084 helix: -0.80 (0.77), residues: 32 sheet: -0.21 (0.25), residues: 482 loop : -2.23 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 16 TYR 0.015 0.001 TYR C 152 PHE 0.010 0.001 PHE A 100 TRP 0.015 0.001 TRP D 32 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 8707) covalent geometry : angle 0.63698 (11834) SS BOND : bond 0.00559 ( 10) SS BOND : angle 1.70111 ( 20) hydrogen bonds : bond 0.03622 ( 240) hydrogen bonds : angle 5.61851 ( 681) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 110 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 83 MET cc_start: 0.5252 (ptt) cc_final: 0.4646 (mtm) REVERT: B 55 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8368 (tm-30) REVERT: C 124 LYS cc_start: 0.9169 (ttmt) cc_final: 0.8760 (mtpt) REVERT: C 204 ASN cc_start: 0.8541 (p0) cc_final: 0.8330 (p0) REVERT: D 151 ASP cc_start: 0.6136 (m-30) cc_final: 0.5905 (m-30) REVERT: D 210 ASN cc_start: 0.6319 (t0) cc_final: 0.5627 (p0) outliers start: 50 outliers final: 34 residues processed: 153 average time/residue: 0.0916 time to fit residues: 19.8310 Evaluate side-chains 139 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 217 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 39 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 64 optimal weight: 0.0060 chunk 100 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 79 optimal weight: 0.0060 chunk 83 optimal weight: 0.9990 overall best weight: 1.2018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.138661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.101956 restraints weight = 15486.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.104506 restraints weight = 10402.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.106010 restraints weight = 8286.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.106991 restraints weight = 7253.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.107228 restraints weight = 6689.008| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8717 Z= 0.144 Angle : 0.631 7.279 11854 Z= 0.326 Chirality : 0.044 0.143 1301 Planarity : 0.005 0.043 1519 Dihedral : 4.692 26.654 1190 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.59 % Favored : 90.31 % Rotamer: Outliers : 4.32 % Allowed : 24.55 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % 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: -1.80 (0.25), residues: 1084 helix: -0.87 (0.77), residues: 32 sheet: -0.11 (0.25), residues: 456 loop : -2.18 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 16 TYR 0.017 0.001 TYR C 152 PHE 0.010 0.001 PHE L 28 TRP 0.015 0.001 TRP D 32 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8707) covalent geometry : angle 0.62904 (11834) SS BOND : bond 0.00524 ( 10) SS BOND : angle 1.48285 ( 20) hydrogen bonds : bond 0.03310 ( 240) hydrogen bonds : angle 5.49012 ( 681) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 107 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.5349 (ptt) cc_final: 0.4803 (mtm) REVERT: C 124 LYS cc_start: 0.9237 (ttmt) cc_final: 0.8836 (mtpt) REVERT: C 151 ASP cc_start: 0.7001 (t0) cc_final: 0.6793 (t0) REVERT: D 151 ASP cc_start: 0.6299 (m-30) cc_final: 0.6035 (m-30) REVERT: D 197 THR cc_start: 0.8459 (OUTLIER) cc_final: 0.8131 (p) REVERT: D 210 ASN cc_start: 0.6364 (t0) cc_final: 0.5662 (p0) REVERT: H 43 LYS cc_start: 0.8107 (mmtt) cc_final: 0.7765 (mmtp) outliers start: 41 outliers final: 34 residues processed: 141 average time/residue: 0.0947 time to fit residues: 18.7514 Evaluate side-chains 138 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 103 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 217 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 48 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 0.0980 chunk 41 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.136423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.099302 restraints weight = 15765.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.101961 restraints weight = 11630.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.102369 restraints weight = 8939.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.103614 restraints weight = 8021.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.103718 restraints weight = 7453.753| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8717 Z= 0.221 Angle : 0.690 7.852 11854 Z= 0.361 Chirality : 0.046 0.151 1301 Planarity : 0.005 0.045 1519 Dihedral : 5.011 26.428 1190 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.99 % Favored : 87.92 % Rotamer: Outliers : 5.16 % Allowed : 24.76 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % 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: -1.93 (0.25), residues: 1084 helix: -0.94 (0.78), residues: 32 sheet: -0.14 (0.25), residues: 462 loop : -2.36 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 96 TYR 0.021 0.002 TYR C 152 PHE 0.013 0.002 PHE A 100 TRP 0.018 0.001 TRP D 32 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 8707) covalent geometry : angle 0.68631 (11834) SS BOND : bond 0.00630 ( 10) SS BOND : angle 1.91874 ( 20) hydrogen bonds : bond 0.04128 ( 240) hydrogen bonds : angle 5.73834 ( 681) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 107 time to evaluate : 0.344 Fit side-chains REVERT: A 83 MET cc_start: 0.5448 (ptt) cc_final: 0.4753 (mtm) REVERT: C 124 LYS cc_start: 0.9259 (ttmt) cc_final: 0.8867 (mtpt) REVERT: D 151 ASP cc_start: 0.6397 (m-30) cc_final: 0.6091 (m-30) REVERT: D 210 ASN cc_start: 0.6532 (t0) cc_final: 0.5793 (p0) REVERT: H 16 ARG cc_start: 0.7589 (mmp-170) cc_final: 0.7325 (mmp-170) REVERT: H 43 LYS cc_start: 0.8277 (mmtt) cc_final: 0.7972 (mmtp) outliers start: 49 outliers final: 36 residues processed: 150 average time/residue: 0.0888 time to fit residues: 19.0704 Evaluate side-chains 142 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 217 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 50 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 89 optimal weight: 0.0070 chunk 40 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.138207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.103310 restraints weight = 15569.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.104331 restraints weight = 10907.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.104260 restraints weight = 8732.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.104350 restraints weight = 8969.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.104870 restraints weight = 8486.213| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8717 Z= 0.144 Angle : 0.649 7.909 11854 Z= 0.335 Chirality : 0.044 0.141 1301 Planarity : 0.005 0.045 1519 Dihedral : 4.795 26.884 1190 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.32 % Favored : 90.59 % Rotamer: Outliers : 4.21 % Allowed : 26.03 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % 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: -1.90 (0.25), residues: 1084 helix: -0.86 (0.79), residues: 32 sheet: -0.13 (0.25), residues: 456 loop : -2.30 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 211 TYR 0.016 0.001 TYR C 152 PHE 0.010 0.001 PHE C 173 TRP 0.015 0.001 TRP D 32 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8707) covalent geometry : angle 0.64539 (11834) SS BOND : bond 0.00495 ( 10) SS BOND : angle 1.79631 ( 20) hydrogen bonds : bond 0.03269 ( 240) hydrogen bonds : angle 5.47985 ( 681) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 16 ARG cc_start: 0.6782 (ttp-170) cc_final: 0.6093 (tpp80) REVERT: A 83 MET cc_start: 0.5497 (ptt) cc_final: 0.4835 (mtm) REVERT: B 90 GLU cc_start: 0.8296 (pp20) cc_final: 0.8006 (pp20) REVERT: C 124 LYS cc_start: 0.9249 (ttmt) cc_final: 0.8840 (mtpt) REVERT: D 151 ASP cc_start: 0.6295 (m-30) cc_final: 0.6078 (m-30) REVERT: D 210 ASN cc_start: 0.6343 (t0) cc_final: 0.5777 (p0) REVERT: H 16 ARG cc_start: 0.7610 (mmp-170) cc_final: 0.7384 (mmp-170) REVERT: H 43 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7885 (mmtp) outliers start: 40 outliers final: 34 residues processed: 144 average time/residue: 0.1012 time to fit residues: 20.6055 Evaluate side-chains 139 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 98 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 94 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.136576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.099857 restraints weight = 15600.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.102253 restraints weight = 10564.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.103766 restraints weight = 8458.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.104587 restraints weight = 7411.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.104854 restraints weight = 6855.750| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8717 Z= 0.209 Angle : 0.710 8.318 11854 Z= 0.368 Chirality : 0.046 0.149 1301 Planarity : 0.005 0.045 1519 Dihedral : 5.032 26.463 1190 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.08 % Favored : 87.82 % Rotamer: Outliers : 4.53 % Allowed : 26.03 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % 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 (0.25), residues: 1084 helix: -0.82 (0.79), residues: 32 sheet: -0.13 (0.25), residues: 458 loop : -2.42 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 211 TYR 0.015 0.002 TYR C 152 PHE 0.012 0.002 PHE A 100 TRP 0.017 0.001 TRP D 32 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 8707) covalent geometry : angle 0.70508 (11834) SS BOND : bond 0.00566 ( 10) SS BOND : angle 2.17406 ( 20) hydrogen bonds : bond 0.03942 ( 240) hydrogen bonds : angle 5.69889 ( 681) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 106 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 16 ARG cc_start: 0.6646 (ttp-170) cc_final: 0.6099 (tpp80) REVERT: A 83 MET cc_start: 0.5443 (ptt) cc_final: 0.4845 (mtm) REVERT: B 90 GLU cc_start: 0.8369 (pp20) cc_final: 0.8109 (pp20) REVERT: C 124 LYS cc_start: 0.9231 (ttmt) cc_final: 0.8841 (mtpt) REVERT: D 151 ASP cc_start: 0.6410 (m-30) cc_final: 0.6136 (m-30) REVERT: D 210 ASN cc_start: 0.6492 (t0) cc_final: 0.5849 (p0) REVERT: H 16 ARG cc_start: 0.7613 (mmp-170) cc_final: 0.7361 (mmp-170) REVERT: H 43 LYS cc_start: 0.8253 (mmtt) cc_final: 0.7973 (mmtp) outliers start: 43 outliers final: 39 residues processed: 142 average time/residue: 0.0881 time to fit residues: 17.7553 Evaluate side-chains 144 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 105 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 81 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 67 optimal weight: 0.0970 chunk 35 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.139013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.102472 restraints weight = 15634.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.105058 restraints weight = 10456.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.106699 restraints weight = 8310.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.107516 restraints weight = 7219.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.108217 restraints weight = 6676.118| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8717 Z= 0.120 Angle : 0.644 8.232 11854 Z= 0.329 Chirality : 0.044 0.139 1301 Planarity : 0.005 0.046 1519 Dihedral : 4.680 27.167 1190 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 3.06 % Allowed : 27.82 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % 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: -1.87 (0.25), residues: 1084 helix: -0.87 (0.81), residues: 32 sheet: -0.08 (0.25), residues: 451 loop : -2.29 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 211 TYR 0.021 0.001 TYR C 152 PHE 0.009 0.001 PHE L 28 TRP 0.015 0.001 TRP D 32 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8707) covalent geometry : angle 0.64117 (11834) SS BOND : bond 0.00472 ( 10) SS BOND : angle 1.68305 ( 20) hydrogen bonds : bond 0.02869 ( 240) hydrogen bonds : angle 5.33618 ( 681) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 16 ARG cc_start: 0.6635 (ttp-170) cc_final: 0.6202 (ttp80) REVERT: A 83 MET cc_start: 0.5234 (ptt) cc_final: 0.4825 (mtm) REVERT: B 90 GLU cc_start: 0.8271 (pp20) cc_final: 0.8043 (pp20) REVERT: C 124 LYS cc_start: 0.9217 (ttmt) cc_final: 0.8853 (mtpt) REVERT: C 151 ASP cc_start: 0.6856 (t0) cc_final: 0.6022 (t0) REVERT: C 204 ASN cc_start: 0.8578 (p0) cc_final: 0.8176 (p0) REVERT: D 210 ASN cc_start: 0.6235 (t0) cc_final: 0.5678 (p0) REVERT: H 16 ARG cc_start: 0.7507 (mmp-170) cc_final: 0.7167 (mmp-170) REVERT: H 43 LYS cc_start: 0.8062 (mmtt) cc_final: 0.7757 (mttp) REVERT: L 148 TRP cc_start: 0.8160 (m100) cc_final: 0.7897 (m100) outliers start: 29 outliers final: 25 residues processed: 139 average time/residue: 0.0910 time to fit residues: 17.7534 Evaluate side-chains 132 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 16 optimal weight: 4.9990 chunk 73 optimal weight: 0.2980 chunk 77 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 51 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 28 optimal weight: 0.0270 chunk 48 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.141296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.105484 restraints weight = 15518.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.108087 restraints weight = 10328.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.109706 restraints weight = 8146.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.110736 restraints weight = 7084.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.111239 restraints weight = 6505.237| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8717 Z= 0.114 Angle : 0.638 7.869 11854 Z= 0.328 Chirality : 0.044 0.139 1301 Planarity : 0.005 0.046 1519 Dihedral : 4.471 26.674 1190 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 2.32 % Allowed : 28.24 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % 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: -1.79 (0.25), residues: 1084 helix: -0.85 (0.82), residues: 32 sheet: -0.00 (0.25), residues: 445 loop : -2.24 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 211 TYR 0.016 0.001 TYR C 152 PHE 0.017 0.001 PHE L 139 TRP 0.013 0.001 TRP D 32 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8707) covalent geometry : angle 0.63426 (11834) SS BOND : bond 0.00501 ( 10) SS BOND : angle 1.73294 ( 20) hydrogen bonds : bond 0.02645 ( 240) hydrogen bonds : angle 5.13278 ( 681) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1765.45 seconds wall clock time: 31 minutes 16.92 seconds (1876.92 seconds total)