Starting phenix.real_space_refine on Sun Dec 29 15:43:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ek1_28192/12_2024/8ek1_28192.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ek1_28192/12_2024/8ek1_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_28192/12_2024/8ek1_28192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ek1_28192/12_2024/8ek1_28192.map" model { file = "/net/cci-nas-00/data/ceres_data/8ek1_28192/12_2024/8ek1_28192.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ek1_28192/12_2024/8ek1_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.51, per 1000 atoms: 0.65 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: 2.03 Conformation dependent library (CDL) restraints added in 1.0 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: 1.18 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: 2.18 Time building geometry restraints manager: 2.39 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: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.020 Find NCS groups from input model: 0.240 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: 28.890 ------------------------------------------------------------------------------- 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 : 1.021 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: 0.2553 time to fit residues: 39.3585 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 : 1.026 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 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 : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 124 LYS cc_start: 0.9238 (ttmt) cc_final: 0.8802 (mtpt) REVERT: C 151 ASP cc_start: 0.7153 (t0) cc_final: 0.6550 (t0) REVERT: D 79 GLN cc_start: 0.7715 (mt0) cc_final: 0.7246 (pm20) REVERT: D 151 ASP cc_start: 0.6449 (m-30) cc_final: 0.6117 (m-30) REVERT: D 210 ASN cc_start: 0.6623 (t0) cc_final: 0.5917 (p0) outliers start: 43 outliers final: 20 residues processed: 147 average time/residue: 0.2049 time to fit residues: 41.4467 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 : 0.953 ------------------------------------------------------------------------------- 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 54 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 105 optimal weight: 0.0870 chunk 86 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8707 Z= 0.222 Angle : 0.624 7.317 11834 Z= 0.326 Chirality : 0.044 0.146 1301 Planarity : 0.005 0.060 1519 Dihedral : 4.844 26.954 1190 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.23 % Favored : 90.68 % Rotamer: Outliers : 4.85 % Allowed : 23.50 % 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: -1.93 (0.25), residues: 1084 helix: -0.63 (0.81), residues: 32 sheet: -0.23 (0.25), residues: 481 loop : -2.34 (0.24), residues: 571 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 0.010 0.001 PHE L 28 TYR 0.025 0.001 TYR C 152 ARG 0.002 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 160 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 114 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: C 124 LYS cc_start: 0.9236 (ttmt) cc_final: 0.8806 (mtpt) REVERT: C 151 ASP cc_start: 0.7014 (t0) cc_final: 0.6484 (t0) REVERT: D 79 GLN cc_start: 0.7415 (mt0) cc_final: 0.6957 (pm20) REVERT: D 151 ASP cc_start: 0.6378 (m-30) cc_final: 0.6083 (m-30) REVERT: D 187 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8012 (mm-30) REVERT: D 210 ASN cc_start: 0.6734 (t0) cc_final: 0.5983 (p0) REVERT: H 43 LYS cc_start: 0.8379 (mmtt) cc_final: 0.7686 (mttp) outliers start: 46 outliers final: 27 residues processed: 155 average time/residue: 0.2073 time to fit residues: 44.3596 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 : 1.034 ------------------------------------------------------------------------------- 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 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 82 GLN 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 96 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8707 Z= 0.214 Angle : 0.615 7.165 11834 Z= 0.319 Chirality : 0.044 0.143 1301 Planarity : 0.005 0.056 1519 Dihedral : 4.725 26.852 1190 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.96 % Favored : 89.94 % Rotamer: Outliers : 5.37 % Allowed : 23.18 % 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: -1.87 (0.25), residues: 1084 helix: -0.74 (0.78), residues: 32 sheet: -0.20 (0.25), residues: 481 loop : -2.27 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 32 HIS 0.005 0.001 HIS H 35 PHE 0.010 0.001 PHE L 28 TYR 0.014 0.001 TYR C 152 ARG 0.003 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 163 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 112 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 124 LYS cc_start: 0.9224 (ttmt) cc_final: 0.8797 (mtpt) REVERT: C 204 ASN cc_start: 0.8529 (p0) cc_final: 0.8303 (p0) REVERT: D 151 ASP cc_start: 0.6410 (m-30) cc_final: 0.6137 (m-30) REVERT: D 187 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8070 (mm-30) REVERT: D 210 ASN cc_start: 0.6708 (t0) cc_final: 0.5963 (p0) REVERT: H 43 LYS cc_start: 0.8389 (mmtt) cc_final: 0.7750 (mttp) outliers start: 51 outliers final: 32 residues processed: 157 average time/residue: 0.2074 time to fit residues: 44.6548 Evaluate side-chains 142 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 93 SER 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 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 82 GLN Chi-restraints excluded: chain H residue 115 LEU 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 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 86 optimal weight: 0.3980 chunk 58 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 77 optimal weight: 0.2980 chunk 42 optimal weight: 0.6980 chunk 88 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8707 Z= 0.210 Angle : 0.616 7.530 11834 Z= 0.318 Chirality : 0.044 0.144 1301 Planarity : 0.005 0.051 1519 Dihedral : 4.665 26.588 1190 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.04 % Favored : 90.87 % 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: -1.79 (0.25), residues: 1084 helix: -0.80 (0.78), residues: 32 sheet: -0.08 (0.25), residues: 456 loop : -2.21 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 32 HIS 0.004 0.001 HIS H 35 PHE 0.010 0.001 PHE L 28 TYR 0.033 0.001 TYR C 152 ARG 0.002 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 162 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 114 time to evaluate : 0.972 Fit side-chains REVERT: C 124 LYS cc_start: 0.9231 (ttmt) cc_final: 0.8811 (mtpt) REVERT: C 204 ASN cc_start: 0.8533 (p0) cc_final: 0.8318 (p0) REVERT: D 151 ASP cc_start: 0.6374 (m-30) cc_final: 0.6106 (m-30) REVERT: D 210 ASN cc_start: 0.6714 (t0) cc_final: 0.5971 (p0) outliers start: 48 outliers final: 35 residues processed: 155 average time/residue: 0.1949 time to fit residues: 41.9469 Evaluate side-chains 143 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 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 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 89 GLU Chi-restraints excluded: chain H residue 115 LEU 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 105 GLU 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 34 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 60 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8707 Z= 0.304 Angle : 0.674 7.739 11834 Z= 0.352 Chirality : 0.045 0.146 1301 Planarity : 0.005 0.050 1519 Dihedral : 4.959 26.502 1190 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.62 % Favored : 88.28 % Rotamer: Outliers : 5.58 % Allowed : 24.45 % Favored : 69.97 % 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: -0.90 (0.77), residues: 32 sheet: -0.12 (0.25), residues: 462 loop : -2.35 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 32 HIS 0.005 0.001 HIS H 35 PHE 0.013 0.002 PHE A 100 TYR 0.017 0.002 TYR C 152 ARG 0.004 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 162 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 109 time to evaluate : 1.001 Fit side-chains REVERT: A 83 MET cc_start: 0.5416 (ptt) cc_final: 0.4703 (mtm) REVERT: C 89 GLU cc_start: 0.7742 (mp0) cc_final: 0.7541 (mp0) REVERT: C 124 LYS cc_start: 0.9239 (ttmt) cc_final: 0.8821 (mtpt) REVERT: D 151 ASP cc_start: 0.6448 (m-30) cc_final: 0.6128 (m-30) REVERT: D 210 ASN cc_start: 0.6735 (t0) cc_final: 0.6019 (p0) REVERT: H 43 LYS cc_start: 0.8402 (mmtt) cc_final: 0.8052 (mmtp) outliers start: 53 outliers final: 35 residues processed: 155 average time/residue: 0.1865 time to fit residues: 41.1604 Evaluate side-chains 143 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 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 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 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 11 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 63 optimal weight: 0.0970 chunk 41 optimal weight: 20.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8707 Z= 0.249 Angle : 0.644 7.954 11834 Z= 0.334 Chirality : 0.045 0.142 1301 Planarity : 0.005 0.044 1519 Dihedral : 4.822 26.661 1190 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.96 % Favored : 89.94 % Rotamer: Outliers : 4.32 % Allowed : 26.03 % Favored : 69.65 % 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: -1.91 (0.25), residues: 1084 helix: -0.82 (0.79), residues: 32 sheet: -0.13 (0.25), residues: 456 loop : -2.32 (0.24), residues: 596 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 0.017 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 154 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 113 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 16 ARG cc_start: 0.6789 (ttp-170) cc_final: 0.6104 (tpp80) REVERT: A 83 MET cc_start: 0.5408 (ptt) cc_final: 0.4737 (mtm) REVERT: C 124 LYS cc_start: 0.9241 (ttmt) cc_final: 0.8825 (mtpt) REVERT: D 151 ASP cc_start: 0.6482 (m-30) cc_final: 0.6201 (m-30) REVERT: D 210 ASN cc_start: 0.6725 (t0) cc_final: 0.6063 (p0) REVERT: H 16 ARG cc_start: 0.7614 (mmp-170) cc_final: 0.7313 (mmp-170) REVERT: H 43 LYS cc_start: 0.8329 (mmtt) cc_final: 0.7992 (mmtp) outliers start: 41 outliers final: 35 residues processed: 148 average time/residue: 0.2000 time to fit residues: 41.1680 Evaluate side-chains 143 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 77 ASN 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 37 VAL 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 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 62 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 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 61 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1889 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= 0.191 Angle : 0.630 7.783 11834 Z= 0.324 Chirality : 0.044 0.141 1301 Planarity : 0.005 0.045 1519 Dihedral : 4.662 26.854 1190 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.41 % Favored : 90.50 % Rotamer: Outliers : 3.16 % Allowed : 27.71 % 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 (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: -1.83 (0.25), residues: 1084 helix: -0.85 (0.80), residues: 32 sheet: -0.08 (0.25), residues: 456 loop : -2.26 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 32 HIS 0.004 0.001 HIS C 35 PHE 0.009 0.001 PHE L 28 TYR 0.019 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 141 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 16 ARG cc_start: 0.6701 (ttp-170) cc_final: 0.6258 (ttp80) REVERT: A 83 MET cc_start: 0.5457 (ptt) cc_final: 0.4851 (mtm) REVERT: C 124 LYS cc_start: 0.9211 (ttmt) cc_final: 0.8796 (mtpt) REVERT: C 204 ASN cc_start: 0.8615 (p0) cc_final: 0.8342 (p0) REVERT: D 151 ASP cc_start: 0.6456 (m-30) cc_final: 0.6236 (m-30) REVERT: D 210 ASN cc_start: 0.6511 (t0) cc_final: 0.5971 (p0) REVERT: H 16 ARG cc_start: 0.7572 (mmp-170) cc_final: 0.7364 (mmp-170) REVERT: H 43 LYS cc_start: 0.8259 (mmtt) cc_final: 0.7770 (mttp) outliers start: 30 outliers final: 24 residues processed: 138 average time/residue: 0.2207 time to fit residues: 41.9009 Evaluate side-chains 132 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 50 VAL 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 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 96 CYS Chi-restraints excluded: chain H residue 212 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 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 90 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 57 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN L 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.089 8707 Z= 0.562 Angle : 0.814 8.532 11834 Z= 0.430 Chirality : 0.050 0.178 1301 Planarity : 0.006 0.049 1519 Dihedral : 5.569 26.402 1190 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.75 % Favored : 86.16 % Rotamer: Outliers : 4.53 % Allowed : 26.77 % Favored : 68.70 % 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: -2.21 (0.25), residues: 1084 helix: -0.88 (0.79), residues: 32 sheet: -0.32 (0.25), residues: 472 loop : -2.61 (0.24), residues: 580 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 0.019 0.002 PHE A 100 TYR 0.022 0.003 TYR A 95 ARG 0.003 0.001 ARG L 96 *********************** 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 150 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 107 time to evaluate : 0.831 Fit side-chains REVERT: C 124 LYS cc_start: 0.9253 (ttmt) cc_final: 0.8846 (mtpt) REVERT: C 151 ASP cc_start: 0.7126 (t0) cc_final: 0.6601 (t0) REVERT: D 151 ASP cc_start: 0.6677 (m-30) cc_final: 0.6354 (m-30) REVERT: D 210 ASN cc_start: 0.7078 (t0) cc_final: 0.6311 (p0) REVERT: H 16 ARG cc_start: 0.7686 (mmp-170) cc_final: 0.7407 (mmp-170) REVERT: H 43 LYS cc_start: 0.8519 (mmtt) cc_final: 0.8311 (mmtp) REVERT: H 151 ASP cc_start: 0.7570 (m-30) cc_final: 0.7237 (m-30) outliers start: 43 outliers final: 34 residues processed: 146 average time/residue: 0.2323 time to fit residues: 46.4961 Evaluate side-chains 136 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 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 83 MET Chi-restraints excluded: chain H residue 176 VAL 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 62 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2125 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= 0.203 Angle : 0.671 8.350 11834 Z= 0.347 Chirality : 0.045 0.144 1301 Planarity : 0.005 0.046 1519 Dihedral : 4.937 27.227 1190 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 2.63 % Allowed : 28.87 % Favored : 68.49 % 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: -2.06 (0.25), residues: 1084 helix: -0.82 (0.83), residues: 32 sheet: -0.24 (0.25), residues: 464 loop : -2.45 (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 C 35 PHE 0.008 0.001 PHE A 53 TYR 0.022 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 135 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: A 16 ARG cc_start: 0.6733 (ttp-170) cc_final: 0.6061 (tpp80) REVERT: A 83 MET cc_start: 0.5251 (ptt) cc_final: 0.4562 (mtm) REVERT: C 124 LYS cc_start: 0.9228 (ttmt) cc_final: 0.8821 (mtpt) REVERT: C 151 ASP cc_start: 0.6887 (t0) cc_final: 0.6105 (t0) REVERT: C 204 ASN cc_start: 0.8671 (p0) cc_final: 0.8364 (p0) REVERT: D 151 ASP cc_start: 0.6396 (m-30) cc_final: 0.6179 (m-30) REVERT: D 210 ASN cc_start: 0.6580 (t0) cc_final: 0.6051 (p0) REVERT: H 16 ARG cc_start: 0.7540 (mmp-170) cc_final: 0.7180 (mmp-170) outliers start: 25 outliers final: 24 residues processed: 133 average time/residue: 0.2043 time to fit residues: 38.0162 Evaluate side-chains 134 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 83 MET Chi-restraints excluded: chain H residue 177 LEU 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 55 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 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 0.0980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.137566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.101162 restraints weight = 15415.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.103669 restraints weight = 10396.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.105239 restraints weight = 8313.532| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8707 Z= 0.244 Angle : 0.681 7.978 11834 Z= 0.354 Chirality : 0.045 0.145 1301 Planarity : 0.005 0.045 1519 Dihedral : 4.870 26.462 1190 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer: Outliers : 3.06 % Allowed : 27.92 % 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: -2.02 (0.25), residues: 1084 helix: -0.88 (0.82), residues: 32 sheet: -0.21 (0.25), residues: 464 loop : -2.42 (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 L 28 TYR 0.016 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: 1904.19 seconds wall clock time: 35 minutes 37.96 seconds (2137.96 seconds total)