Starting phenix.real_space_refine on Tue Jul 29 00:23:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ek1_28192/07_2025/8ek1_28192.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ek1_28192/07_2025/8ek1_28192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ek1_28192/07_2025/8ek1_28192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ek1_28192/07_2025/8ek1_28192.map" model { file = "/net/cci-nas-00/data/ceres_data/8ek1_28192/07_2025/8ek1_28192.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ek1_28192/07_2025/8ek1_28192.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2884 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 5364 2.51 5 N 1438 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 5.68, per 1000 atoms: 0.67 Number of scatterers: 8497 At special positions: 0 Unit cell: (78.2, 126.96, 147.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1663 8.00 N 1438 7.00 C 5364 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 147 " - pdb=" SG CYS C 203 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 1.1 seconds 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 25 sheets defined 3.6% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 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: 2.37 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: 18.740 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.680 Find NCS groups from input model: 0.250 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8717 Z= 0.198 Angle : 0.740 7.623 11854 Z= 0.417 Chirality : 0.046 0.246 1301 Planarity : 0.005 0.042 1519 Dihedral : 15.719 87.423 3105 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.23 % Favored : 90.31 % Rotamer: Outliers : 0.53 % Allowed : 27.19 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.18018 ( 240) hydrogen bonds : angle 7.61778 ( 681) SS BOND : bond 0.00432 ( 10) SS BOND : angle 2.15680 ( 20) covalent geometry : bond 0.00378 ( 8707) covalent geometry : angle 0.73550 (11834) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.816 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: 0.2370 time to fit residues: 36.4529 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 : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain D residue 209 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 83 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 HIS H 178 GLN ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.130519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3273 r_free = 0.3273 target = 0.095004 restraints weight = 15255.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.096027 restraints weight = 13330.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.096026 restraints weight = 11334.559| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 8717 Z= 0.249 Angle : 0.705 7.751 11854 Z= 0.375 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 Details of bonding type rmsd hydrogen bonds : bond 0.04858 ( 240) hydrogen bonds : angle 6.36192 ( 681) SS BOND : bond 0.00686 ( 10) SS BOND : angle 1.67787 ( 20) covalent geometry : bond 0.00602 ( 8707) covalent geometry : angle 0.70270 (11834) *********************** 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 : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 124 LYS cc_start: 0.9173 (ttmt) cc_final: 0.8723 (mtpt) REVERT: C 151 ASP cc_start: 0.7089 (t0) cc_final: 0.6495 (t0) REVERT: D 79 GLN cc_start: 0.7436 (mt0) cc_final: 0.7118 (pm20) REVERT: D 151 ASP cc_start: 0.6152 (m-30) cc_final: 0.5848 (m-30) REVERT: D 210 ASN cc_start: 0.6210 (t0) cc_final: 0.5578 (p0) outliers start: 43 outliers final: 20 residues processed: 147 average time/residue: 0.2117 time to fit residues: 42.6321 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 : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 201 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 77 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 GLN L 158 ASN L 189 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.133791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.098809 restraints weight = 15348.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.098817 restraints weight = 13024.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.098817 restraints weight = 12955.349| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8717 Z= 0.129 Angle : 0.613 7.205 11854 Z= 0.319 Chirality : 0.044 0.146 1301 Planarity : 0.005 0.056 1519 Dihedral : 4.765 27.020 1190 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.67 % Favored : 91.24 % Rotamer: Outliers : 4.43 % Allowed : 23.92 % 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: -1.90 (0.25), residues: 1084 helix: -0.65 (0.81), residues: 32 sheet: -0.22 (0.25), residues: 481 loop : -2.31 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 32 HIS 0.005 0.001 HIS C 35 PHE 0.010 0.001 PHE L 28 TYR 0.026 0.001 TYR C 152 ARG 0.002 0.000 ARG D 211 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 240) hydrogen bonds : angle 5.79492 ( 681) SS BOND : bond 0.00586 ( 10) SS BOND : angle 1.41012 ( 20) covalent geometry : bond 0.00302 ( 8707) covalent geometry : angle 0.61050 (11834) *********************** 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 159 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 117 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: C 124 LYS cc_start: 0.9230 (ttmt) cc_final: 0.8794 (mtpt) REVERT: C 151 ASP cc_start: 0.7023 (t0) cc_final: 0.6504 (t0) REVERT: D 79 GLN cc_start: 0.7122 (mt0) cc_final: 0.6513 (pm20) REVERT: D 151 ASP cc_start: 0.6103 (m-30) cc_final: 0.5853 (m-30) REVERT: D 187 GLU cc_start: 0.8558 (mm-30) cc_final: 0.7974 (mm-30) REVERT: D 210 ASN cc_start: 0.6327 (t0) cc_final: 0.5659 (p0) REVERT: H 43 LYS cc_start: 0.8225 (mmtt) cc_final: 0.7492 (mttp) outliers start: 42 outliers final: 24 residues processed: 155 average time/residue: 0.2026 time to fit residues: 43.6829 Evaluate side-chains 135 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain 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 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 33 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 3 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.130858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3295 r_free = 0.3295 target = 0.096190 restraints weight = 15400.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.096905 restraints weight = 13138.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.097131 restraints weight = 11333.815| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8717 Z= 0.196 Angle : 0.666 7.629 11854 Z= 0.349 Chirality : 0.045 0.145 1301 Planarity : 0.005 0.057 1519 Dihedral : 4.972 26.696 1190 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.62 % Favored : 88.28 % Rotamer: Outliers : 5.27 % Allowed : 23.39 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.92 (0.25), residues: 1084 helix: -0.76 (0.77), residues: 32 sheet: -0.14 (0.25), residues: 467 loop : -2.37 (0.24), residues: 585 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 0.012 0.002 PHE A 100 TYR 0.015 0.002 TYR C 152 ARG 0.003 0.000 ARG H 16 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 240) hydrogen bonds : angle 5.89977 ( 681) SS BOND : bond 0.00612 ( 10) SS BOND : angle 1.69227 ( 20) covalent geometry : bond 0.00472 ( 8707) covalent geometry : angle 0.66280 (11834) *********************** 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 157 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 107 time to evaluate : 1.148 Fit side-chains REVERT: A 83 MET cc_start: 0.5393 (ptt) cc_final: 0.4782 (mtm) REVERT: C 124 LYS cc_start: 0.9196 (ttmt) cc_final: 0.8768 (mtpt) REVERT: C 204 ASN cc_start: 0.8502 (p0) cc_final: 0.8208 (p0) REVERT: D 151 ASP cc_start: 0.6129 (m-30) cc_final: 0.5877 (m-30) REVERT: D 210 ASN cc_start: 0.6290 (t0) cc_final: 0.5631 (p0) outliers start: 50 outliers final: 33 residues processed: 152 average time/residue: 0.2163 time to fit residues: 45.6470 Evaluate side-chains 138 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 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 C residue 185 LEU Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 167 ASP 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 29 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 16 optimal weight: 0.1980 chunk 61 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.130772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.098897 restraints weight = 15341.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.098224 restraints weight = 19461.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099482 restraints weight = 17913.938| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8717 Z= 0.206 Angle : 0.681 7.876 11854 Z= 0.356 Chirality : 0.046 0.145 1301 Planarity : 0.005 0.057 1519 Dihedral : 5.084 26.794 1190 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.89 % Favored : 89.02 % Rotamer: Outliers : 6.11 % Allowed : 23.71 % Favored : 70.18 % 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: -2.01 (0.25), residues: 1084 helix: -0.87 (0.78), residues: 32 sheet: -0.24 (0.25), residues: 483 loop : -2.43 (0.24), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 32 HIS 0.006 0.001 HIS H 35 PHE 0.012 0.002 PHE A 100 TYR 0.014 0.002 TYR A 95 ARG 0.002 0.000 ARG H 16 Details of bonding type rmsd hydrogen bonds : bond 0.04063 ( 240) hydrogen bonds : angle 5.86230 ( 681) SS BOND : bond 0.00583 ( 10) SS BOND : angle 1.80162 ( 20) covalent geometry : bond 0.00497 ( 8707) covalent geometry : angle 0.67789 (11834) *********************** 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 170 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 112 time to evaluate : 1.531 Fit side-chains REVERT: A 83 MET cc_start: 0.5522 (ptt) cc_final: 0.4990 (mtm) REVERT: C 124 LYS cc_start: 0.9094 (ttmt) cc_final: 0.8637 (mtpt) REVERT: C 151 ASP cc_start: 0.6963 (t0) cc_final: 0.6424 (t0) REVERT: C 204 ASN cc_start: 0.8397 (p0) cc_final: 0.8113 (p0) REVERT: D 210 ASN cc_start: 0.5824 (t0) cc_final: 0.5414 (p0) REVERT: H 43 LYS cc_start: 0.8367 (mmtt) cc_final: 0.7930 (mmtp) outliers start: 58 outliers final: 38 residues processed: 163 average time/residue: 0.2379 time to fit residues: 53.7471 Evaluate side-chains 147 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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 C residue 185 LEU Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 217 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 3 optimal weight: 7.9990 chunk 39 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 0.0980 chunk 68 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.138840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.103034 restraints weight = 15431.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.104725 restraints weight = 10905.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.105407 restraints weight = 8544.221| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8717 Z= 0.123 Angle : 0.618 7.568 11854 Z= 0.321 Chirality : 0.044 0.142 1301 Planarity : 0.005 0.050 1519 Dihedral : 4.743 27.119 1190 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.32 % Favored : 90.59 % Rotamer: Outliers : 4.95 % Allowed : 25.61 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.94 (0.25), residues: 1084 helix: -0.90 (0.79), residues: 32 sheet: -0.22 (0.25), residues: 480 loop : -2.35 (0.24), residues: 572 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 0.010 0.001 PHE L 28 TYR 0.017 0.001 TYR C 152 ARG 0.002 0.000 ARG D 211 Details of bonding type rmsd hydrogen bonds : bond 0.03047 ( 240) hydrogen bonds : angle 5.50872 ( 681) SS BOND : bond 0.00578 ( 10) SS BOND : angle 1.56216 ( 20) covalent geometry : bond 0.00290 ( 8707) covalent geometry : angle 0.61558 (11834) *********************** 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 163 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 116 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 16 ARG cc_start: 0.6785 (ttp-170) cc_final: 0.6102 (tpp80) REVERT: A 83 MET cc_start: 0.5382 (ptt) cc_final: 0.4751 (mtm) REVERT: C 124 LYS cc_start: 0.9255 (ttmt) cc_final: 0.8829 (mtpt) REVERT: C 204 ASN cc_start: 0.8476 (p0) cc_final: 0.8227 (p0) REVERT: D 210 ASN cc_start: 0.6305 (t0) cc_final: 0.5658 (p0) REVERT: H 16 ARG cc_start: 0.7596 (mmp-170) cc_final: 0.7352 (mmp-170) REVERT: H 43 LYS cc_start: 0.8237 (mmtt) cc_final: 0.7734 (mttp) outliers start: 47 outliers final: 31 residues processed: 155 average time/residue: 0.2626 time to fit residues: 55.6068 Evaluate side-chains 138 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 217 LYS Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 65 optimal weight: 0.9980 chunk 57 optimal weight: 20.0000 chunk 95 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.137659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.102561 restraints weight = 15624.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.103831 restraints weight = 10555.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.103809 restraints weight = 8607.763| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8717 Z= 0.154 Angle : 0.653 7.418 11854 Z= 0.339 Chirality : 0.045 0.142 1301 Planarity : 0.005 0.045 1519 Dihedral : 4.806 26.412 1190 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.70 % Favored : 89.21 % Rotamer: Outliers : 4.43 % Allowed : 26.24 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.25), residues: 1084 helix: -0.88 (0.80), residues: 32 sheet: -0.12 (0.25), residues: 465 loop : -2.34 (0.24), residues: 587 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 29 TYR 0.017 0.001 TYR C 152 ARG 0.002 0.000 ARG D 211 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 240) hydrogen bonds : angle 5.50843 ( 681) SS BOND : bond 0.00538 ( 10) SS BOND : angle 1.84103 ( 20) covalent geometry : bond 0.00370 ( 8707) covalent geometry : angle 0.64929 (11834) *********************** 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: 42 poor density : 112 time to evaluate : 1.275 Fit side-chains revert: symmetry clash REVERT: A 16 ARG cc_start: 0.6659 (ttp-170) cc_final: 0.6018 (tpp80) REVERT: A 83 MET cc_start: 0.5509 (ptt) cc_final: 0.4777 (mtm) REVERT: C 124 LYS cc_start: 0.9250 (ttmt) cc_final: 0.8837 (mtpt) REVERT: C 204 ASN cc_start: 0.8481 (p0) cc_final: 0.8230 (p0) REVERT: D 210 ASN cc_start: 0.6340 (t0) cc_final: 0.5701 (p0) outliers start: 42 outliers final: 34 residues processed: 148 average time/residue: 0.2603 time to fit residues: 53.8366 Evaluate side-chains 142 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 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 11 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 217 LYS 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 24 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 71 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 chunk 89 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.140129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.104312 restraints weight = 15755.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.106265 restraints weight = 11416.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.107000 restraints weight = 8902.425| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8717 Z= 0.116 Angle : 0.639 8.128 11854 Z= 0.326 Chirality : 0.044 0.140 1301 Planarity : 0.005 0.046 1519 Dihedral : 4.611 26.837 1190 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.86 % Favored : 91.05 % Rotamer: Outliers : 3.48 % Allowed : 27.61 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.25), residues: 1084 helix: -0.96 (0.80), residues: 32 sheet: -0.05 (0.25), residues: 456 loop : -2.23 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 32 HIS 0.004 0.001 HIS C 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 Details of bonding type rmsd hydrogen bonds : bond 0.02776 ( 240) hydrogen bonds : angle 5.29166 ( 681) SS BOND : bond 0.00457 ( 10) SS BOND : angle 1.66256 ( 20) covalent geometry : bond 0.00276 ( 8707) covalent geometry : angle 0.63552 (11834) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 1.352 Fit side-chains revert: symmetry clash REVERT: A 16 ARG cc_start: 0.6610 (ttp-170) cc_final: 0.6144 (ttp80) REVERT: A 83 MET cc_start: 0.5524 (ptt) cc_final: 0.4923 (mtm) REVERT: C 124 LYS cc_start: 0.9222 (ttmt) cc_final: 0.8800 (mtpt) REVERT: C 204 ASN cc_start: 0.8492 (p0) cc_final: 0.8219 (p0) REVERT: D 210 ASN cc_start: 0.6170 (t0) cc_final: 0.5571 (p0) REVERT: H 43 LYS cc_start: 0.8017 (mmtt) cc_final: 0.7601 (mttp) REVERT: L 148 TRP cc_start: 0.8232 (m100) cc_final: 0.7979 (m100) outliers start: 33 outliers final: 26 residues processed: 144 average time/residue: 0.2194 time to fit residues: 43.6461 Evaluate side-chains 135 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain D residue 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 89 GLU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 217 LYS Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 89 optimal weight: 0.0040 chunk 12 optimal weight: 0.0050 chunk 36 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 95 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.3406 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.141886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.106565 restraints weight = 15727.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.108645 restraints weight = 10752.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.109122 restraints weight = 8288.118| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8717 Z= 0.113 Angle : 0.635 9.935 11854 Z= 0.324 Chirality : 0.044 0.137 1301 Planarity : 0.005 0.046 1519 Dihedral : 4.395 26.629 1190 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.39 % Favored : 91.51 % Rotamer: Outliers : 3.27 % Allowed : 27.50 % Favored : 69.23 % 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: -1.69 (0.25), residues: 1084 helix: -0.89 (0.83), residues: 32 sheet: 0.02 (0.25), residues: 453 loop : -2.15 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 32 HIS 0.004 0.001 HIS C 35 PHE 0.017 0.001 PHE L 139 TYR 0.016 0.001 TYR C 152 ARG 0.001 0.000 ARG D 142 Details of bonding type rmsd hydrogen bonds : bond 0.02556 ( 240) hydrogen bonds : angle 5.07807 ( 681) SS BOND : bond 0.00438 ( 10) SS BOND : angle 1.52303 ( 20) covalent geometry : bond 0.00270 ( 8707) covalent geometry : angle 0.63224 (11834) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 1.461 Fit side-chains revert: symmetry clash REVERT: A 16 ARG cc_start: 0.6527 (ttp-170) cc_final: 0.5852 (tpp80) REVERT: A 83 MET cc_start: 0.5486 (ptt) cc_final: 0.4906 (mtm) REVERT: C 124 LYS cc_start: 0.9206 (ttmt) cc_final: 0.8811 (mtpt) REVERT: C 204 ASN cc_start: 0.8450 (p0) cc_final: 0.8212 (p0) REVERT: D 187 GLU cc_start: 0.8593 (mm-30) cc_final: 0.7866 (mm-30) REVERT: D 210 ASN cc_start: 0.6273 (t0) cc_final: 0.5640 (p0) REVERT: H 43 LYS cc_start: 0.8003 (mmtt) cc_final: 0.7620 (mttp) REVERT: L 148 TRP cc_start: 0.8166 (m100) cc_final: 0.7926 (m100) outliers start: 31 outliers final: 27 residues processed: 146 average time/residue: 0.2337 time to fit residues: 47.4760 Evaluate side-chains 139 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 176 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 37 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 88 optimal weight: 0.2980 chunk 87 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.138203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.102078 restraints weight = 15664.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.104710 restraints weight = 10772.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.105074 restraints weight = 8554.164| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8717 Z= 0.141 Angle : 0.671 9.387 11854 Z= 0.345 Chirality : 0.044 0.141 1301 Planarity : 0.005 0.046 1519 Dihedral : 4.528 26.207 1190 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 2.74 % Allowed : 28.45 % 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: -1.78 (0.25), residues: 1084 helix: -0.96 (0.80), residues: 32 sheet: -0.06 (0.25), residues: 460 loop : -2.23 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 32 HIS 0.005 0.001 HIS C 35 PHE 0.017 0.001 PHE L 139 TYR 0.020 0.001 TYR C 152 ARG 0.001 0.000 ARG D 211 Details of bonding type rmsd hydrogen bonds : bond 0.03191 ( 240) hydrogen bonds : angle 5.13911 ( 681) SS BOND : bond 0.00480 ( 10) SS BOND : angle 1.56153 ( 20) covalent geometry : bond 0.00339 ( 8707) covalent geometry : angle 0.66835 (11834) ********************** 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 140 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 1.751 Fit side-chains revert: symmetry clash REVERT: A 16 ARG cc_start: 0.6549 (ttp-170) cc_final: 0.5901 (tpp80) REVERT: A 34 MET cc_start: 0.8008 (tpp) cc_final: 0.7333 (mtt) REVERT: A 83 MET cc_start: 0.5444 (ptt) cc_final: 0.4827 (mtm) REVERT: C 124 LYS cc_start: 0.9200 (ttmt) cc_final: 0.8811 (mtpt) REVERT: C 204 ASN cc_start: 0.8469 (p0) cc_final: 0.8226 (p0) REVERT: D 187 GLU cc_start: 0.8602 (mm-30) cc_final: 0.7844 (mm-30) REVERT: D 195 GLU cc_start: 0.7517 (tm-30) cc_final: 0.6196 (tt0) REVERT: D 210 ASN cc_start: 0.6205 (t0) cc_final: 0.5509 (p0) REVERT: H 43 LYS cc_start: 0.8040 (mmtt) cc_final: 0.7688 (mttp) REVERT: L 148 TRP cc_start: 0.8195 (m100) cc_final: 0.7877 (m100) outliers start: 26 outliers final: 26 residues processed: 137 average time/residue: 0.2593 time to fit residues: 50.4657 Evaluate side-chains 138 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR 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 93 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 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 176 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 88 optimal weight: 0.0670 chunk 19 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 106 optimal weight: 0.0870 chunk 17 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.131361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.103060 restraints weight = 15835.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.102030 restraints weight = 25795.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.101895 restraints weight = 22290.907| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8717 Z= 0.123 Angle : 0.660 9.198 11854 Z= 0.338 Chirality : 0.044 0.137 1301 Planarity : 0.005 0.047 1519 Dihedral : 4.432 26.548 1190 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 3.27 % Allowed : 27.92 % 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: -1.75 (0.25), residues: 1084 helix: -1.07 (0.78), residues: 32 sheet: 0.00 (0.25), residues: 455 loop : -2.21 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 32 HIS 0.004 0.001 HIS L 198 PHE 0.017 0.001 PHE L 139 TYR 0.018 0.001 TYR C 152 ARG 0.001 0.000 ARG D 211 Details of bonding type rmsd hydrogen bonds : bond 0.02785 ( 240) hydrogen bonds : angle 5.01581 ( 681) SS BOND : bond 0.00454 ( 10) SS BOND : angle 1.41373 ( 20) covalent geometry : bond 0.00293 ( 8707) covalent geometry : angle 0.65838 (11834) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3842.29 seconds wall clock time: 72 minutes 23.81 seconds (4343.81 seconds total)