Starting phenix.real_space_refine on Fri Mar 15 10:30:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ek1_28192/03_2024/8ek1_28192.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ek1_28192/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ek1_28192/03_2024/8ek1_28192.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ek1_28192/03_2024/8ek1_28192.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ek1_28192/03_2024/8ek1_28192.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ek1_28192/03_2024/8ek1_28192.pdb" } 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 Residue "A GLU 46": "OE1" <-> "OE2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "D GLU 143": "OE1" <-> "OE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H GLU 219": "OE1" <-> "OE2" Residue "L GLU 90": "OE1" <-> "OE2" Residue "L GLU 143": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.22, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 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: 3.01 Conformation dependent library (CDL) restraints added in 1.7 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: 1.07 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: 2.27 Time building geometry restraints manager: 3.33 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: 98.78 - 105.83: 209 105.83 - 112.88: 4621 112.88 - 119.93: 2713 119.93 - 126.98: 4169 126.98 - 134.03: 122 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 2.520 nonbonded pdb=" NH1 ARG A 67 " pdb=" O ASP A 84 " model vdw 2.218 2.520 nonbonded pdb=" O PHE D 62 " pdb=" OG1 THR D 74 " model vdw 2.227 2.440 nonbonded pdb=" O SER H 195 " pdb=" OG1 THR H 198 " model vdw 2.230 2.440 nonbonded pdb=" O GLN D 124 " pdb=" OG SER D 127 " model vdw 2.263 2.440 ... (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 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: 1.640 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: 7.280 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 26.310 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.680 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 1.123 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: 0.2502 time to fit residues: 38.2281 Evaluate side-chains 111 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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: 2.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 chunk 83 optimal weight: 0.0030 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- 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** ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8707 Z= 0.208 Angle : 0.599 7.290 11834 Z= 0.314 Chirality : 0.044 0.153 1301 Planarity : 0.005 0.082 1519 Dihedral : 4.857 33.685 1192 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.06 % Favored : 89.85 % Rotamer: Outliers : 4.11 % Allowed : 24.24 % 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: -1.80 (0.25), residues: 1084 helix: -0.25 (0.87), residues: 32 sheet: -0.03 (0.26), residues: 450 loop : -2.28 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 32 HIS 0.004 0.001 HIS H 35 PHE 0.010 0.001 PHE L 28 TYR 0.011 0.001 TYR A 95 ARG 0.002 0.000 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 157 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 118 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 LYS cc_start: 0.9252 (ttmt) cc_final: 0.8823 (mtpt) REVERT: C 151 ASP cc_start: 0.7023 (t0) cc_final: 0.6408 (t0) REVERT: C 152 TYR cc_start: 0.8733 (p90) cc_final: 0.8499 (p90) REVERT: D 79 GLN cc_start: 0.7630 (mt0) cc_final: 0.7254 (pm20) REVERT: D 210 ASN cc_start: 0.6577 (t0) cc_final: 0.6062 (p0) REVERT: H 43 LYS cc_start: 0.8537 (mmtt) cc_final: 0.7842 (mttp) outliers start: 39 outliers final: 18 residues processed: 151 average time/residue: 0.2303 time to fit residues: 46.8543 Evaluate side-chains 129 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 150 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 66 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 105 optimal weight: 0.2980 chunk 86 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1061 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 : 0.597 7.285 11834 Z= 0.309 Chirality : 0.043 0.146 1301 Planarity : 0.005 0.056 1519 Dihedral : 4.666 26.399 1190 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.41 % Favored : 90.50 % Rotamer: Outliers : 4.00 % Allowed : 24.97 % Favored : 71.02 % 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: -1.72 (0.25), residues: 1084 helix: -0.31 (0.83), residues: 32 sheet: 0.05 (0.26), residues: 446 loop : -2.23 (0.24), residues: 606 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 0.011 0.001 TYR A 95 ARG 0.004 0.000 ARG H 16 *********************** 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 152 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 114 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 124 LYS cc_start: 0.9241 (ttmt) cc_final: 0.8827 (mtpt) REVERT: D 79 GLN cc_start: 0.7692 (mt0) cc_final: 0.7043 (pm20) REVERT: D 187 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8158 (mm-30) REVERT: D 197 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8133 (p) REVERT: D 210 ASN cc_start: 0.6678 (t0) cc_final: 0.6049 (p0) REVERT: H 43 LYS cc_start: 0.8571 (mmtt) cc_final: 0.7905 (mttp) outliers start: 38 outliers final: 24 residues processed: 147 average time/residue: 0.2064 time to fit residues: 41.9409 Evaluate side-chains 137 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 112 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 15 VAL 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 1 GLN 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 96 CYS 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 105 GLU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1351 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= 0.267 Angle : 0.629 7.422 11834 Z= 0.327 Chirality : 0.044 0.146 1301 Planarity : 0.005 0.046 1519 Dihedral : 4.820 26.373 1190 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.79 % Favored : 89.11 % Rotamer: Outliers : 4.95 % Allowed : 24.45 % Favored : 70.60 % 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: -0.30 (0.83), residues: 32 sheet: -0.08 (0.25), residues: 471 loop : -2.29 (0.24), residues: 581 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 A 100 TYR 0.029 0.002 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 159 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 112 time to evaluate : 1.024 Fit side-chains REVERT: C 124 LYS cc_start: 0.9228 (ttmt) cc_final: 0.8819 (mtpt) REVERT: C 204 ASN cc_start: 0.8535 (p0) cc_final: 0.8284 (p0) REVERT: D 187 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8156 (mm-30) REVERT: D 210 ASN cc_start: 0.6865 (t0) cc_final: 0.6125 (p0) outliers start: 47 outliers final: 28 residues processed: 152 average time/residue: 0.2011 time to fit residues: 42.2635 Evaluate side-chains 138 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 110 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 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 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 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 185 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 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: 3.9990 chunk 58 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8707 Z= 0.317 Angle : 0.659 7.739 11834 Z= 0.344 Chirality : 0.045 0.145 1301 Planarity : 0.005 0.057 1519 Dihedral : 4.989 26.586 1190 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.35 % Favored : 88.56 % Rotamer: Outliers : 5.06 % Allowed : 25.08 % Favored : 69.86 % 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: -1.84 (0.26), residues: 1084 helix: -0.38 (0.81), residues: 32 sheet: -0.06 (0.25), residues: 468 loop : -2.37 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 32 HIS 0.005 0.001 HIS H 35 PHE 0.013 0.002 PHE A 100 TYR 0.015 0.002 TYR C 152 ARG 0.003 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 159 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 111 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: C 89 GLU cc_start: 0.7918 (mp0) cc_final: 0.7478 (mp0) REVERT: C 124 LYS cc_start: 0.9237 (ttmt) cc_final: 0.8838 (mtpt) REVERT: C 204 ASN cc_start: 0.8510 (p0) cc_final: 0.8274 (p0) REVERT: D 210 ASN cc_start: 0.6829 (t0) cc_final: 0.6097 (p0) REVERT: H 43 LYS cc_start: 0.8499 (mmtt) cc_final: 0.8099 (mmtp) outliers start: 48 outliers final: 30 residues processed: 153 average time/residue: 0.1898 time to fit residues: 40.8962 Evaluate side-chains 138 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 108 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 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 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 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 184 SER 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 170 ASP 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: 0.9990 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 chunk 103 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1705 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= 0.253 Angle : 0.632 7.485 11834 Z= 0.326 Chirality : 0.045 0.143 1301 Planarity : 0.005 0.045 1519 Dihedral : 4.864 26.736 1190 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.24 % Favored : 89.67 % Rotamer: Outliers : 4.85 % Allowed : 25.61 % Favored : 69.55 % 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: -0.39 (0.80), residues: 32 sheet: 0.01 (0.26), residues: 447 loop : -2.35 (0.23), residues: 605 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 0.016 0.001 TYR C 152 ARG 0.001 0.000 ARG A 87 *********************** 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 155 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 109 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: A 16 ARG cc_start: 0.6763 (ttp-170) cc_final: 0.6089 (tpp80) REVERT: C 89 GLU cc_start: 0.7920 (mp0) cc_final: 0.7462 (mp0) REVERT: C 124 LYS cc_start: 0.9247 (ttmt) cc_final: 0.8843 (mtpt) REVERT: C 204 ASN cc_start: 0.8498 (p0) cc_final: 0.8283 (p0) REVERT: D 151 ASP cc_start: 0.6684 (m-30) cc_final: 0.6406 (m-30) REVERT: D 210 ASN cc_start: 0.6756 (t0) cc_final: 0.6071 (p0) outliers start: 46 outliers final: 36 residues processed: 149 average time/residue: 0.1771 time to fit residues: 37.1678 Evaluate side-chains 144 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 108 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 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 C residue 5 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain D residue 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 184 SER 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 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 0.2980 chunk 58 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 47 optimal weight: 0.0870 chunk 63 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1733 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= 0.181 Angle : 0.593 7.306 11834 Z= 0.305 Chirality : 0.044 0.142 1301 Planarity : 0.005 0.044 1519 Dihedral : 4.628 26.719 1190 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.32 % Favored : 90.59 % Rotamer: Outliers : 4.32 % Allowed : 26.87 % Favored : 68.81 % 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: -1.76 (0.25), residues: 1084 helix: -0.41 (0.81), residues: 32 sheet: 0.06 (0.26), residues: 448 loop : -2.31 (0.24), residues: 604 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 L 28 TYR 0.019 0.001 TYR C 152 ARG 0.002 0.000 ARG A 87 *********************** 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 fitting. rotamer outliers: 41 poor density : 113 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: A 16 ARG cc_start: 0.6715 (ttp-170) cc_final: 0.6045 (tpp80) REVERT: C 89 GLU cc_start: 0.7906 (mp0) cc_final: 0.7428 (mp0) REVERT: C 124 LYS cc_start: 0.9223 (ttmt) cc_final: 0.8808 (mtpt) REVERT: C 204 ASN cc_start: 0.8502 (p0) cc_final: 0.8274 (p0) REVERT: D 151 ASP cc_start: 0.6556 (m-30) cc_final: 0.6295 (m-30) REVERT: D 197 THR cc_start: 0.8412 (OUTLIER) cc_final: 0.8082 (p) REVERT: D 210 ASN cc_start: 0.6590 (t0) cc_final: 0.6022 (p0) REVERT: H 16 ARG cc_start: 0.7512 (mmp-170) cc_final: 0.7296 (mmp-170) REVERT: H 43 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7583 (mttp) outliers start: 41 outliers final: 33 residues processed: 149 average time/residue: 0.2001 time to fit residues: 40.9431 Evaluate side-chains 140 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 106 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 50 VAL 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 83 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 65 SER 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 96 CYS Chi-restraints excluded: chain H residue 184 SER 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 15 VAL 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 170 ASP 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: 5.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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: 0.8169 moved from start: 0.1873 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= 0.248 Angle : 0.642 9.688 11834 Z= 0.329 Chirality : 0.044 0.143 1301 Planarity : 0.005 0.044 1519 Dihedral : 4.752 26.282 1190 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.98 % Favored : 88.93 % Rotamer: Outliers : 4.32 % Allowed : 26.87 % Favored : 68.81 % 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: -1.84 (0.25), residues: 1084 helix: -0.62 (0.77), residues: 32 sheet: -0.00 (0.26), residues: 449 loop : -2.34 (0.23), residues: 603 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 0.010 0.001 PHE A 100 TYR 0.019 0.001 TYR C 152 ARG 0.001 0.000 ARG A 87 *********************** 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 151 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 110 time to evaluate : 1.082 Fit side-chains revert: symmetry clash REVERT: A 16 ARG cc_start: 0.6645 (ttp-170) cc_final: 0.6016 (tpp80) REVERT: C 89 GLU cc_start: 0.7902 (mp0) cc_final: 0.7424 (mp0) REVERT: C 124 LYS cc_start: 0.9232 (ttmt) cc_final: 0.8831 (mtpt) REVERT: C 204 ASN cc_start: 0.8488 (p0) cc_final: 0.8279 (p0) REVERT: D 151 ASP cc_start: 0.6612 (m-30) cc_final: 0.6346 (m-30) REVERT: D 210 ASN cc_start: 0.6743 (t0) cc_final: 0.6044 (p0) REVERT: H 43 LYS cc_start: 0.8332 (mmtt) cc_final: 0.8013 (mmtp) REVERT: L 211 ARG cc_start: 0.8424 (ttp80) cc_final: 0.8199 (ttp-170) outliers start: 41 outliers final: 37 residues processed: 147 average time/residue: 0.2002 time to fit residues: 40.2808 Evaluate side-chains 145 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 108 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 70 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 83 VAL 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 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 83 MET Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL 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 170 ASP 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: 4.9990 chunk 96 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN H 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 8707 Z= 0.530 Angle : 0.803 9.732 11834 Z= 0.421 Chirality : 0.049 0.172 1301 Planarity : 0.006 0.048 1519 Dihedral : 5.551 26.368 1190 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.21 % Favored : 85.61 % Rotamer: Outliers : 4.53 % Allowed : 27.61 % Favored : 67.86 % 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: -2.14 (0.25), residues: 1084 helix: -0.85 (0.76), residues: 32 sheet: -0.10 (0.26), residues: 445 loop : -2.63 (0.23), residues: 607 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 0.020 0.002 PHE A 100 TYR 0.025 0.003 TYR C 152 ARG 0.003 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 106 time to evaluate : 1.144 Fit side-chains REVERT: C 89 GLU cc_start: 0.8031 (mp0) cc_final: 0.7614 (mp0) REVERT: C 124 LYS cc_start: 0.9252 (ttmt) cc_final: 0.8843 (mtpt) REVERT: C 151 ASP cc_start: 0.7066 (t0) cc_final: 0.6545 (t0) REVERT: D 151 ASP cc_start: 0.6784 (m-30) cc_final: 0.6454 (m-30) REVERT: H 43 LYS cc_start: 0.8502 (mmtt) cc_final: 0.8124 (mmtp) REVERT: H 151 ASP cc_start: 0.7566 (m-30) cc_final: 0.7248 (m-30) outliers start: 43 outliers final: 35 residues processed: 143 average time/residue: 0.2108 time to fit residues: 41.4583 Evaluate side-chains 137 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 102 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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 57 ASN 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 C residue 5 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain D residue 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 83 MET Chi-restraints excluded: chain H residue 184 SER 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 170 ASP Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8707 Z= 0.214 Angle : 0.658 10.121 11834 Z= 0.337 Chirality : 0.044 0.141 1301 Planarity : 0.005 0.044 1519 Dihedral : 4.930 26.996 1190 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.69 % Favored : 90.22 % Rotamer: Outliers : 3.69 % Allowed : 28.24 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.25), residues: 1084 helix: -0.88 (0.76), residues: 32 sheet: 0.05 (0.26), residues: 427 loop : -2.54 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 32 HIS 0.005 0.001 HIS C 35 PHE 0.010 0.001 PHE C 173 TYR 0.019 0.001 TYR C 152 ARG 0.002 0.000 ARG A 87 ********************** 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 143 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 108 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 16 ARG cc_start: 0.6707 (ttp-170) cc_final: 0.6296 (ttp80) REVERT: C 89 GLU cc_start: 0.7961 (mp0) cc_final: 0.7450 (mp0) REVERT: C 124 LYS cc_start: 0.9234 (ttmt) cc_final: 0.8804 (mtpt) REVERT: C 151 ASP cc_start: 0.6897 (t0) cc_final: 0.6355 (t0) REVERT: D 151 ASP cc_start: 0.6628 (m-30) cc_final: 0.6362 (m-30) REVERT: D 210 ASN cc_start: 0.6806 (t0) cc_final: 0.6060 (p0) REVERT: H 43 LYS cc_start: 0.8268 (mmtt) cc_final: 0.7911 (mttp) REVERT: L 22 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8699 (p) outliers start: 35 outliers final: 32 residues processed: 139 average time/residue: 0.1899 time to fit residues: 36.5587 Evaluate side-chains 139 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 106 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 70 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain D residue 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 184 SER 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 15 VAL 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 170 ASP Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.9990 chunk 78 optimal weight: 0.0000 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 4 optimal weight: 0.0000 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.141689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.105964 restraints weight = 15445.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.108560 restraints weight = 10395.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.110203 restraints weight = 8201.258| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8707 Z= 0.167 Angle : 0.619 10.285 11834 Z= 0.314 Chirality : 0.043 0.138 1301 Planarity : 0.005 0.045 1519 Dihedral : 4.432 26.717 1190 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.04 % Favored : 90.87 % Rotamer: Outliers : 2.74 % Allowed : 29.50 % Favored : 67.76 % 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: -1.87 (0.25), residues: 1084 helix: -1.06 (0.77), residues: 32 sheet: 0.00 (0.25), residues: 447 loop : -2.35 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 32 HIS 0.004 0.001 HIS C 35 PHE 0.010 0.001 PHE C 100 TYR 0.015 0.001 TYR C 152 ARG 0.003 0.000 ARG H 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1889.02 seconds wall clock time: 34 minutes 47.15 seconds (2087.15 seconds total)