Starting phenix.real_space_refine on Sat Feb 15 00:25:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ek1_28192/02_2025/8ek1_28192.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ek1_28192/02_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_28192/02_2025/8ek1_28192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ek1_28192/02_2025/8ek1_28192.map" model { file = "/net/cci-nas-00/data/ceres_data/8ek1_28192/02_2025/8ek1_28192.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ek1_28192/02_2025/8ek1_28192.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.047 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.66, per 1000 atoms: 0.67 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: 1.93 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.15 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: 2.32 Time building geometry restraints manager: 2.24 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: 5.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 20.990 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.780 ------------------------------------------------------------------------------- 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 8707 Z= 0.246 Angle : 0.736 7.623 11834 Z= 0.415 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (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 TRP 0.018 0.001 TRP L 148 HIS 0.004 0.001 HIS C 35 PHE 0.018 0.001 PHE D 139 TYR 0.015 0.001 TYR C 152 ARG 0.005 0.000 ARG L 211 *********************** 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 : 1.113 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: 0.2506 time to fit residues: 38.3676 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 : 0.948 ------------------------------------------------------------------------------- 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 90 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 83 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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 H 178 GLN ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.130519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.095247 restraints weight = 15255.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.096133 restraints weight = 13162.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.096462 restraints weight = 11954.320| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 8707 Z= 0.395 Angle : 0.703 7.751 11834 Z= 0.374 Chirality : 0.046 0.155 1301 Planarity : 0.006 0.086 1519 Dihedral : 5.297 34.608 1192 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.44 % Favored : 88.47 % Rotamer: Outliers : 4.53 % Allowed : 23.39 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.25), residues: 1084 helix: -0.41 (0.85), residues: 32 sheet: -0.17 (0.25), residues: 468 loop : -2.42 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 32 HIS 0.007 0.002 HIS H 35 PHE 0.015 0.002 PHE A 100 TYR 0.017 0.002 TYR A 95 ARG 0.006 0.001 ARG H 16 *********************** 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 154 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 111 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 124 LYS cc_start: 0.9202 (ttmt) cc_final: 0.8758 (mtpt) REVERT: C 151 ASP cc_start: 0.7129 (t0) cc_final: 0.6528 (t0) REVERT: D 79 GLN cc_start: 0.7435 (mt0) cc_final: 0.7101 (pm20) REVERT: D 151 ASP cc_start: 0.6147 (m-30) cc_final: 0.5838 (m-30) REVERT: D 210 ASN cc_start: 0.6208 (t0) cc_final: 0.5571 (p0) outliers start: 43 outliers final: 20 residues processed: 147 average time/residue: 0.2105 time to fit residues: 42.3812 Evaluate side-chains 126 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 56 SER Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain C residue 37 VAL 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 201 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASP 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 Chi-restraints excluded: chain L residue 201 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 77 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.132470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.097577 restraints weight = 15374.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.098119 restraints weight = 13747.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.098512 restraints weight = 11670.822| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8707 Z= 0.247 Angle : 0.636 7.391 11834 Z= 0.333 Chirality : 0.044 0.146 1301 Planarity : 0.005 0.060 1519 Dihedral : 4.914 26.939 1190 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.41 % Favored : 90.50 % Rotamer: Outliers : 4.95 % Allowed : 23.39 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.25), residues: 1084 helix: -0.63 (0.81), residues: 32 sheet: -0.25 (0.25), residues: 481 loop : -2.37 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 32 HIS 0.005 0.001 HIS H 35 PHE 0.010 0.001 PHE L 28 TYR 0.026 0.001 TYR C 152 ARG 0.003 0.000 ARG D 211 *********************** 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 161 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 114 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: C 124 LYS cc_start: 0.9146 (ttmt) cc_final: 0.8691 (mtpt) REVERT: C 151 ASP cc_start: 0.6946 (t0) cc_final: 0.6447 (t0) REVERT: D 79 GLN cc_start: 0.7122 (mt0) cc_final: 0.6717 (pm20) REVERT: D 151 ASP cc_start: 0.5945 (m-30) cc_final: 0.5699 (m-30) REVERT: D 187 GLU cc_start: 0.8485 (mm-30) cc_final: 0.7869 (mm-30) REVERT: D 210 ASN cc_start: 0.6205 (t0) cc_final: 0.5601 (p0) REVERT: H 43 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7505 (mttp) outliers start: 47 outliers final: 28 residues processed: 156 average time/residue: 0.2087 time to fit residues: 45.2324 Evaluate side-chains 138 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 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 C residue 37 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 122 ASP 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 89 GLU 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 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 3 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 65 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 158 ASN L 189 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.133834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3336 r_free = 0.3336 target = 0.098968 restraints weight = 15330.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.099895 restraints weight = 13199.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.100423 restraints weight = 11365.718| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8707 Z= 0.183 Angle : 0.601 7.012 11834 Z= 0.311 Chirality : 0.044 0.143 1301 Planarity : 0.005 0.055 1519 Dihedral : 4.638 26.954 1190 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.41 % Favored : 90.50 % Rotamer: Outliers : 4.85 % Allowed : 23.71 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.25), residues: 1084 helix: -0.75 (0.78), residues: 32 sheet: -0.22 (0.25), residues: 482 loop : -2.25 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 32 HIS 0.004 0.001 HIS H 35 PHE 0.010 0.001 PHE L 28 TYR 0.012 0.001 TYR C 152 ARG 0.002 0.000 ARG H 16 *********************** 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 160 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 114 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 124 LYS cc_start: 0.9178 (ttmt) cc_final: 0.8742 (mtpt) REVERT: C 204 ASN cc_start: 0.8503 (p0) cc_final: 0.8258 (p0) REVERT: D 151 ASP cc_start: 0.6159 (m-30) cc_final: 0.5924 (m-30) REVERT: D 187 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8015 (mm-30) REVERT: D 210 ASN cc_start: 0.6334 (t0) cc_final: 0.5689 (p0) REVERT: H 43 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7661 (mttp) outliers start: 46 outliers final: 27 residues processed: 153 average time/residue: 0.2157 time to fit residues: 45.3598 Evaluate side-chains 137 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 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 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 82 GLN Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 33 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 29 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 101 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 104 optimal weight: 0.0010 chunk 99 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.7592 ------------------------------------------------------------------------------- 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 = 0.3809 r_free = 0.3809 target = 0.131532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3298 r_free = 0.3298 target = 0.096578 restraints weight = 15398.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.097331 restraints weight = 13588.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.097782 restraints weight = 11738.175| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8707 Z= 0.295 Angle : 0.658 8.087 11834 Z= 0.343 Chirality : 0.045 0.145 1301 Planarity : 0.005 0.055 1519 Dihedral : 4.891 26.329 1190 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.89 % Favored : 89.02 % Rotamer: Outliers : 5.06 % Allowed : 24.13 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.25), residues: 1084 helix: -0.86 (0.77), residues: 32 sheet: -0.10 (0.25), residues: 455 loop : -2.28 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 32 HIS 0.005 0.001 HIS H 35 PHE 0.012 0.002 PHE A 100 TYR 0.016 0.002 TYR C 152 ARG 0.004 0.000 ARG H 16 *********************** 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: 48 poor density : 112 time to evaluate : 0.943 Fit side-chains REVERT: C 124 LYS cc_start: 0.9205 (ttmt) cc_final: 0.8786 (mtpt) REVERT: C 204 ASN cc_start: 0.8546 (p0) cc_final: 0.8314 (p0) REVERT: D 151 ASP cc_start: 0.6202 (m-30) cc_final: 0.5946 (m-30) REVERT: D 210 ASN cc_start: 0.6313 (t0) cc_final: 0.5642 (p0) outliers start: 48 outliers final: 34 residues processed: 154 average time/residue: 0.2003 time to fit residues: 42.8684 Evaluate side-chains 140 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 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 5 VAL 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 C residue 147 CYS Chi-restraints excluded: chain D residue 102 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 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 3 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.130719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 116)---------------| | r_work = 0.3290 r_free = 0.3290 target = 0.095646 restraints weight = 15243.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.096520 restraints weight = 13720.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.097165 restraints weight = 11766.871| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8707 Z= 0.351 Angle : 0.702 7.926 11834 Z= 0.367 Chirality : 0.046 0.149 1301 Planarity : 0.005 0.052 1519 Dihedral : 5.108 26.753 1190 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.08 % Favored : 87.82 % Rotamer: Outliers : 5.27 % Allowed : 25.40 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.25), residues: 1084 helix: -0.97 (0.76), residues: 32 sheet: -0.15 (0.26), residues: 459 loop : -2.41 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 32 HIS 0.006 0.001 HIS H 35 PHE 0.014 0.002 PHE A 100 TYR 0.019 0.002 TYR C 152 ARG 0.005 0.000 ARG H 16 *********************** 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 159 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 109 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: A 83 MET cc_start: 0.5464 (ptt) cc_final: 0.4731 (mtm) REVERT: C 124 LYS cc_start: 0.9198 (ttmt) cc_final: 0.8773 (mtpt) REVERT: C 152 TYR cc_start: 0.8779 (p90) cc_final: 0.8571 (p90) REVERT: C 204 ASN cc_start: 0.8474 (p0) cc_final: 0.8252 (p0) REVERT: D 151 ASP cc_start: 0.6144 (m-30) cc_final: 0.5891 (m-30) REVERT: D 210 ASN cc_start: 0.6297 (t0) cc_final: 0.5655 (p0) REVERT: H 43 LYS cc_start: 0.8341 (mmtt) cc_final: 0.7915 (mmtp) outliers start: 50 outliers final: 36 residues processed: 152 average time/residue: 0.1995 time to fit residues: 42.3990 Evaluate side-chains 143 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 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 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 102 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 62 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 65 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.137394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.100596 restraints weight = 15631.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.103183 restraints weight = 10544.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.104529 restraints weight = 8313.766| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8707 Z= 0.251 Angle : 0.655 8.058 11834 Z= 0.339 Chirality : 0.045 0.142 1301 Planarity : 0.005 0.046 1519 Dihedral : 4.892 26.809 1190 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.78 % Favored : 90.13 % Rotamer: Outliers : 4.53 % Allowed : 25.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.25), residues: 1084 helix: -0.83 (0.78), residues: 32 sheet: -0.16 (0.25), residues: 463 loop : -2.39 (0.24), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 32 HIS 0.005 0.001 HIS H 35 PHE 0.011 0.001 PHE C 173 TYR 0.014 0.001 TYR C 152 ARG 0.002 0.000 ARG D 211 *********************** 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 153 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 110 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 16 ARG cc_start: 0.6747 (ttp-170) cc_final: 0.6121 (tpp80) REVERT: A 83 MET cc_start: 0.5341 (ptt) cc_final: 0.4719 (mtm) REVERT: C 124 LYS cc_start: 0.9251 (ttmt) cc_final: 0.8843 (mtpt) REVERT: C 204 ASN cc_start: 0.8445 (p0) cc_final: 0.8190 (p0) REVERT: D 151 ASP cc_start: 0.6477 (m-30) cc_final: 0.6218 (m-30) REVERT: D 210 ASN cc_start: 0.6495 (t0) cc_final: 0.5798 (p0) REVERT: H 16 ARG cc_start: 0.7605 (mmp-170) cc_final: 0.7309 (mmp-170) REVERT: H 43 LYS cc_start: 0.8225 (mmtt) cc_final: 0.7885 (mmtp) outliers start: 43 outliers final: 36 residues processed: 148 average time/residue: 0.1841 time to fit residues: 38.4620 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 : 0.896 ------------------------------------------------------------------------------- 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 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 91 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain D residue 65 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 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 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 24 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 0.0070 chunk 13 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.137240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.100775 restraints weight = 15797.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.102996 restraints weight = 10956.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.103649 restraints weight = 8785.713| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8707 Z= 0.255 Angle : 0.675 9.324 11834 Z= 0.347 Chirality : 0.045 0.142 1301 Planarity : 0.005 0.045 1519 Dihedral : 4.890 26.727 1190 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.16 % Favored : 88.75 % Rotamer: Outliers : 4.74 % Allowed : 26.24 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.25), residues: 1084 helix: -0.83 (0.79), residues: 32 sheet: -0.18 (0.25), residues: 464 loop : -2.38 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 32 HIS 0.005 0.001 HIS H 35 PHE 0.010 0.001 PHE C 173 TYR 0.018 0.001 TYR C 152 ARG 0.002 0.000 ARG D 211 *********************** 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 153 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 108 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: A 16 ARG cc_start: 0.6672 (ttp-170) cc_final: 0.6040 (tpp80) REVERT: A 83 MET cc_start: 0.5438 (ptt) cc_final: 0.4713 (mtm) REVERT: C 124 LYS cc_start: 0.9262 (ttmt) cc_final: 0.8852 (mtpt) REVERT: C 204 ASN cc_start: 0.8468 (p0) cc_final: 0.8217 (p0) REVERT: D 151 ASP cc_start: 0.6304 (m-30) cc_final: 0.6081 (m-30) REVERT: D 210 ASN cc_start: 0.6343 (t0) cc_final: 0.5786 (p0) REVERT: H 43 LYS cc_start: 0.8211 (mmtt) cc_final: 0.7946 (mmtp) outliers start: 45 outliers final: 39 residues processed: 147 average time/residue: 0.2018 time to fit residues: 41.4891 Evaluate side-chains 146 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 107 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 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 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 65 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 176 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 89 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 67 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 51 optimal weight: 0.0470 chunk 95 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.139772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.103905 restraints weight = 15866.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.105377 restraints weight = 11789.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.106493 restraints weight = 10178.277| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8707 Z= 0.212 Angle : 0.664 9.702 11834 Z= 0.339 Chirality : 0.044 0.141 1301 Planarity : 0.005 0.045 1519 Dihedral : 4.754 26.736 1190 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.69 % Favored : 90.22 % Rotamer: Outliers : 4.11 % Allowed : 26.87 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.25), residues: 1084 helix: -0.94 (0.80), residues: 32 sheet: -0.15 (0.25), residues: 464 loop : -2.33 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 32 HIS 0.004 0.001 HIS C 35 PHE 0.009 0.001 PHE C 173 TYR 0.019 0.001 TYR C 152 ARG 0.002 0.000 ARG D 211 *********************** 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 153 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 16 ARG cc_start: 0.6661 (ttp-170) cc_final: 0.6200 (ttp80) REVERT: A 62 ASP cc_start: 0.8050 (m-30) cc_final: 0.7575 (m-30) REVERT: A 83 MET cc_start: 0.5490 (ptt) cc_final: 0.4800 (mtm) REVERT: C 124 LYS cc_start: 0.9252 (ttmt) cc_final: 0.8833 (mtpt) REVERT: C 204 ASN cc_start: 0.8452 (p0) cc_final: 0.8210 (p0) REVERT: D 151 ASP cc_start: 0.6319 (m-30) cc_final: 0.6106 (m-30) REVERT: D 210 ASN cc_start: 0.6271 (t0) cc_final: 0.5709 (p0) REVERT: H 43 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7697 (mttp) outliers start: 39 outliers final: 36 residues processed: 149 average time/residue: 0.2066 time to fit residues: 42.6263 Evaluate side-chains 148 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL 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 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 91 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain D residue 65 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 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 176 VAL 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 146 VAL Chi-restraints excluded: chain L residue 150 VAL 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 37 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.3981 r_free = 0.3981 target = 0.138361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.102663 restraints weight = 15541.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.104648 restraints weight = 10793.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.104880 restraints weight = 9082.944| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8707 Z= 0.227 Angle : 0.672 10.070 11834 Z= 0.345 Chirality : 0.044 0.141 1301 Planarity : 0.005 0.045 1519 Dihedral : 4.763 26.434 1190 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.07 % Favored : 88.93 % Rotamer: Outliers : 4.00 % Allowed : 26.98 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.25), residues: 1084 helix: -0.94 (0.80), residues: 32 sheet: -0.15 (0.25), residues: 464 loop : -2.33 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 32 HIS 0.005 0.001 HIS H 35 PHE 0.009 0.001 PHE C 100 TYR 0.017 0.001 TYR C 152 ARG 0.002 0.000 ARG D 211 ********************** 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 153 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 16 ARG cc_start: 0.6663 (ttp-170) cc_final: 0.6005 (tpp80) REVERT: A 83 MET cc_start: 0.5535 (ptt) cc_final: 0.4810 (mtm) REVERT: B 90 GLU cc_start: 0.8336 (pp20) cc_final: 0.8077 (pp20) REVERT: C 124 LYS cc_start: 0.9248 (ttmt) cc_final: 0.8847 (mtpt) REVERT: C 204 ASN cc_start: 0.8457 (p0) cc_final: 0.8225 (p0) REVERT: D 151 ASP cc_start: 0.6335 (m-30) cc_final: 0.6122 (m-30) REVERT: D 210 ASN cc_start: 0.6373 (t0) cc_final: 0.5724 (p0) REVERT: H 43 LYS cc_start: 0.8244 (mmtt) cc_final: 0.7799 (mttp) outliers start: 38 outliers final: 35 residues processed: 149 average time/residue: 0.2044 time to fit residues: 42.1553 Evaluate side-chains 145 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL 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 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 93 SER 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 15 VAL Chi-restraints excluded: chain D residue 65 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 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 117 THR Chi-restraints excluded: chain H residue 176 VAL 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 146 VAL Chi-restraints excluded: chain L residue 150 VAL 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 88 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.137757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.102863 restraints weight = 15706.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.104043 restraints weight = 11016.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.103992 restraints weight = 8623.849| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8707 Z= 0.254 Angle : 0.688 10.014 11834 Z= 0.354 Chirality : 0.045 0.145 1301 Planarity : 0.005 0.046 1519 Dihedral : 4.842 26.279 1190 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 3.90 % Allowed : 27.19 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.25), residues: 1084 helix: -0.91 (0.80), residues: 32 sheet: -0.17 (0.25), residues: 464 loop : -2.37 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 32 HIS 0.005 0.001 HIS H 35 PHE 0.009 0.001 PHE C 173 TYR 0.021 0.001 TYR C 152 ARG 0.002 0.000 ARG D 211 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2944.67 seconds wall clock time: 53 minutes 47.67 seconds (3227.67 seconds total)