Starting phenix.real_space_refine on Wed Mar 4 20:31:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7njx_12426/03_2026/7njx_12426.cif Found real_map, /net/cci-nas-00/data/ceres_data/7njx_12426/03_2026/7njx_12426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7njx_12426/03_2026/7njx_12426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7njx_12426/03_2026/7njx_12426.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7njx_12426/03_2026/7njx_12426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7njx_12426/03_2026/7njx_12426.map" } resolution = 4.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 5 Type Number sf(0) Gaussians S 28 5.16 5 C 5346 2.51 5 N 1316 2.21 5 O 1399 1.98 5 H 8337 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16426 Number of models: 1 Model: "" Number of chains: 12 Chain: "L" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "M" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "N" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "O" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "P" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "Q" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "R" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "S" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "T" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "a" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3767 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "b" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 979 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "d" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 952 Classifications: {'peptide': 61} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 58} Time building chain proxies: 3.07, per 1000 atoms: 0.19 Number of scatterers: 16426 At special positions: 0 Unit cell: (93.79, 81.34, 116.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 O 1399 8.00 N 1316 7.00 C 5346 6.00 H 8337 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 559.5 milliseconds 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1904 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 2 sheets defined 87.9% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'L' and resid 4 through 46 removed outlier: 3.657A pdb=" N ILE L 8 " --> pdb=" O ASP L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 50 Processing helix chain 'L' and resid 51 through 52 No H-bonds generated for 'chain 'L' and resid 51 through 52' Processing helix chain 'L' and resid 53 through 81 removed outlier: 3.986A pdb=" N PHE L 57 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE L 58 " --> pdb=" O PHE L 54 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE L 59 " --> pdb=" O THR L 55 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR L 68 " --> pdb=" O VAL L 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 46 Processing helix chain 'M' and resid 49 through 81 removed outlier: 3.603A pdb=" N PHE M 54 " --> pdb=" O GLN M 50 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) Proline residue: M 56 - end of helix removed outlier: 3.655A pdb=" N ILE M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE M 70 " --> pdb=" O ALA M 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 46 removed outlier: 3.828A pdb=" N ILE N 8 " --> pdb=" O ASP N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 81 removed outlier: 3.991A pdb=" N PHE N 54 " --> pdb=" O GLN N 50 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR N 55 " --> pdb=" O GLY N 51 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 3.629A pdb=" N TYR N 68 " --> pdb=" O VAL N 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 46 removed outlier: 3.624A pdb=" N ILE O 8 " --> pdb=" O ASP O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 78 removed outlier: 4.788A pdb=" N THR O 55 " --> pdb=" O GLY O 51 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 3.714A pdb=" N ALA O 67 " --> pdb=" O LEU O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 46 removed outlier: 3.833A pdb=" N ILE P 8 " --> pdb=" O ASP P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 80 removed outlier: 4.537A pdb=" N ARG P 52 " --> pdb=" O GLU P 48 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE P 54 " --> pdb=" O GLN P 50 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR P 55 " --> pdb=" O GLY P 51 " (cutoff:3.500A) Proline residue: P 56 - end of helix removed outlier: 3.775A pdb=" N ILE P 59 " --> pdb=" O THR P 55 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA P 67 " --> pdb=" O LEU P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 46 removed outlier: 3.503A pdb=" N ILE Q 8 " --> pdb=" O ASP Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 80 removed outlier: 4.999A pdb=" N THR Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) Proline residue: Q 56 - end of helix removed outlier: 3.606A pdb=" N LEU Q 63 " --> pdb=" O ILE Q 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 46 removed outlier: 4.043A pdb=" N ILE R 8 " --> pdb=" O ASP R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 78 removed outlier: 3.800A pdb=" N THR R 55 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Proline residue: R 56 - end of helix removed outlier: 3.994A pdb=" N GLY R 62 " --> pdb=" O PHE R 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 46 removed outlier: 3.563A pdb=" N ILE S 8 " --> pdb=" O ASP S 4 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 81 removed outlier: 4.519A pdb=" N THR S 55 " --> pdb=" O GLY S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 3.507A pdb=" N ASN S 71 " --> pdb=" O ALA S 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 46 removed outlier: 3.730A pdb=" N ILE T 8 " --> pdb=" O ASP T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 82 removed outlier: 3.888A pdb=" N THR T 55 " --> pdb=" O GLY T 51 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 4.946A pdb=" N ALA T 66 " --> pdb=" O GLY T 62 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA T 67 " --> pdb=" O LEU T 63 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR T 68 " --> pdb=" O VAL T 64 " (cutoff:3.500A) Processing helix chain 'a' and resid 29 through 53 Processing helix chain 'a' and resid 60 through 81 Processing helix chain 'a' and resid 88 through 106 removed outlier: 3.845A pdb=" N LEU a 92 " --> pdb=" O PHE a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 107 through 109 No H-bonds generated for 'chain 'a' and resid 107 through 109' Processing helix chain 'a' and resid 126 through 129 Processing helix chain 'a' and resid 130 through 165 removed outlier: 3.972A pdb=" N VAL a 134 " --> pdb=" O ASP a 130 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE a 155 " --> pdb=" O TRP a 151 " (cutoff:3.500A) removed outlier: 9.293A pdb=" N VAL a 156 " --> pdb=" O ARG a 152 " (cutoff:3.500A) Proline residue: a 159 - end of helix Processing helix chain 'a' and resid 167 through 169 No H-bonds generated for 'chain 'a' and resid 167 through 169' Processing helix chain 'a' and resid 170 through 204 removed outlier: 3.552A pdb=" N ILE a 175 " --> pdb=" O ALA a 171 " (cutoff:3.500A) Proline residue: a 182 - end of helix removed outlier: 4.174A pdb=" N ARG a 188 " --> pdb=" O SER a 184 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLY a 196 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA a 201 " --> pdb=" O GLY a 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 207 through 244 removed outlier: 6.100A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix Processing helix chain 'b' and resid 29 through 49 removed outlier: 4.490A pdb=" N LEU b 35 " --> pdb=" O PHE b 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 84 Processing helix chain 'd' and resid 2 through 22 Processing helix chain 'd' and resid 22 through 61 removed outlier: 3.900A pdb=" N VAL d 26 " --> pdb=" O VAL d 22 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 19 through 22 Processing sheet with id=AA2, first strand: chain 'a' and resid 113 through 114 removed outlier: 3.505A pdb=" N TYR a 113 " --> pdb=" O ALA a 121 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA a 121 " --> pdb=" O TYR a 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 780 hydrogen bonds defined for protein. 2331 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: 3.68 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8336 1.03 - 1.23: 2 1.23 - 1.42: 3358 1.42 - 1.62: 4843 1.62 - 1.81: 55 Bond restraints: 16594 Sorted by residual: bond pdb=" CG1 ILE L 30 " pdb=" CD1 ILE L 30 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.67e+00 bond pdb=" CG1 ILE P 26 " pdb=" CD1 ILE P 26 " ideal model delta sigma weight residual 1.513 1.475 0.038 3.90e-02 6.57e+02 9.29e-01 bond pdb=" CG1 ILE S 15 " pdb=" CD1 ILE S 15 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.76e-01 bond pdb=" CG1 ILE T 15 " pdb=" CD1 ILE T 15 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.60e-01 bond pdb=" CG1 ILE Q 26 " pdb=" CD1 ILE Q 26 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.52e-01 ... (remaining 16589 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 29392 1.41 - 2.82: 652 2.82 - 4.23: 62 4.23 - 5.64: 9 5.64 - 7.06: 1 Bond angle restraints: 30116 Sorted by residual: angle pdb=" N VAL R 79 " pdb=" CA VAL R 79 " pdb=" C VAL R 79 " ideal model delta sigma weight residual 113.71 110.83 2.88 9.50e-01 1.11e+00 9.18e+00 angle pdb=" CA TYR a 145 " pdb=" CB TYR a 145 " pdb=" CG TYR a 145 " ideal model delta sigma weight residual 113.90 118.86 -4.96 1.80e+00 3.09e-01 7.59e+00 angle pdb=" CB MET N 21 " pdb=" CG MET N 21 " pdb=" SD MET N 21 " ideal model delta sigma weight residual 112.70 119.76 -7.06 3.00e+00 1.11e-01 5.53e+00 angle pdb=" CA PHE a 213 " pdb=" C PHE a 213 " pdb=" N PRO a 214 " ideal model delta sigma weight residual 120.58 118.92 1.66 7.40e-01 1.83e+00 5.01e+00 angle pdb=" C PHE L 69 " pdb=" N ILE L 70 " pdb=" CA ILE L 70 " ideal model delta sigma weight residual 120.46 117.49 2.97 1.37e+00 5.33e-01 4.71e+00 ... (remaining 30111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 6667 16.75 - 33.50: 626 33.50 - 50.25: 226 50.25 - 67.01: 226 67.01 - 83.76: 14 Dihedral angle restraints: 7759 sinusoidal: 4150 harmonic: 3609 Sorted by residual: dihedral pdb=" CA ASN a 192 " pdb=" CB ASN a 192 " pdb=" CG ASN a 192 " pdb=" OD1 ASN a 192 " ideal model delta sinusoidal sigma weight residual 120.00 -170.68 -69.32 2 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" N ALA T 25 " pdb=" CA ALA T 25 " pdb=" CB ALA T 25 " pdb=" HB3 ALA T 25 " ideal model delta sinusoidal sigma weight residual 180.00 127.39 52.61 3 1.50e+01 4.44e-03 9.13e+00 dihedral pdb=" CA ALA a 186 " pdb=" C ALA a 186 " pdb=" N LEU a 187 " pdb=" CA LEU a 187 " ideal model delta harmonic sigma weight residual 180.00 -164.90 -15.10 0 5.00e+00 4.00e-02 9.12e+00 ... (remaining 7756 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 798 0.026 - 0.051: 275 0.051 - 0.077: 145 0.077 - 0.102: 85 0.102 - 0.128: 19 Chirality restraints: 1322 Sorted by residual: chirality pdb=" CA ILE b 26 " pdb=" N ILE b 26 " pdb=" C ILE b 26 " pdb=" CB ILE b 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILE M 20 " pdb=" N ILE M 20 " pdb=" C ILE M 20 " pdb=" CB ILE M 20 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA ILE Q 26 " pdb=" N ILE Q 26 " pdb=" C ILE Q 26 " pdb=" CB ILE Q 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 ... (remaining 1319 not shown) Planarity restraints: 2495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR L 68 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C TYR L 68 " -0.028 2.00e-02 2.50e+03 pdb=" O TYR L 68 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE L 69 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE L 70 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C ILE L 70 " 0.025 2.00e-02 2.50e+03 pdb=" O ILE L 70 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN L 71 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE b 40 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" C ILE b 40 " -0.024 2.00e-02 2.50e+03 pdb=" O ILE b 40 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL b 41 " 0.008 2.00e-02 2.50e+03 ... (remaining 2492 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1559 2.22 - 2.81: 36132 2.81 - 3.41: 48699 3.41 - 4.00: 60488 4.00 - 4.60: 94682 Nonbonded interactions: 241560 Sorted by model distance: nonbonded pdb=" O PHE T 78 " pdb=" HG1 THR T 82 " model vdw 1.622 2.450 nonbonded pdb=" O PHE S 78 " pdb=" HG1 THR S 82 " model vdw 1.627 2.450 nonbonded pdb=" O PHE P 78 " pdb=" HG1 THR P 82 " model vdw 1.637 2.450 nonbonded pdb=" O MET d 1 " pdb=" H ILE d 5 " model vdw 1.639 2.450 nonbonded pdb=" O PHE R 54 " pdb=" H PHE R 58 " model vdw 1.647 2.450 ... (remaining 241555 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 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 9.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 0.210 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.800 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 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 : 0.003 0.050 8257 Z= 0.148 Angle : 0.519 7.056 11218 Z= 0.289 Chirality : 0.039 0.128 1322 Planarity : 0.004 0.033 1440 Dihedral : 14.389 83.757 2789 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.26), residues: 1094 helix: 1.31 (0.18), residues: 851 sheet: None (None), residues: 0 loop : 0.32 (0.46), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 45 TYR 0.018 0.001 TYR a 145 PHE 0.015 0.001 PHE a 47 TRP 0.010 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8257) covalent geometry : angle 0.51856 (11218) hydrogen bonds : bond 0.15539 ( 780) hydrogen bonds : angle 7.26969 ( 2331) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 21 MET cc_start: 0.7487 (tmm) cc_final: 0.7243 (tmm) REVERT: O 75 MET cc_start: 0.7986 (tmm) cc_final: 0.7752 (tmm) REVERT: P 63 LEU cc_start: 0.9201 (tp) cc_final: 0.8884 (tp) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1415 time to fit residues: 24.1158 Evaluate side-chains 89 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 46 GLN d 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.080029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.074661 restraints weight = 123037.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.076449 restraints weight = 58711.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.077473 restraints weight = 31577.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.078126 restraints weight = 19030.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.078507 restraints weight = 12588.052| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8257 Z= 0.201 Angle : 0.555 5.660 11218 Z= 0.314 Chirality : 0.040 0.128 1322 Planarity : 0.004 0.028 1440 Dihedral : 3.579 15.728 1149 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.25), residues: 1094 helix: 2.11 (0.17), residues: 852 sheet: None (None), residues: 0 loop : 0.30 (0.46), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 45 TYR 0.024 0.002 TYR a 145 PHE 0.014 0.001 PHE S 80 TRP 0.010 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 8257) covalent geometry : angle 0.55541 (11218) hydrogen bonds : bond 0.05700 ( 780) hydrogen bonds : angle 4.97715 ( 2331) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 75 MET cc_start: 0.8282 (tmm) cc_final: 0.8074 (tmm) REVERT: O 21 MET cc_start: 0.7433 (tmm) cc_final: 0.7216 (tmm) REVERT: O 75 MET cc_start: 0.8044 (tmm) cc_final: 0.7703 (tmm) REVERT: P 63 LEU cc_start: 0.9129 (tp) cc_final: 0.8720 (tp) REVERT: Q 21 MET cc_start: 0.8518 (ppp) cc_final: 0.8303 (ppp) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1402 time to fit residues: 23.8774 Evaluate side-chains 87 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 59 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 63 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 30 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 192 ASN a 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.080490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.075052 restraints weight = 123050.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.076836 restraints weight = 58346.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.077836 restraints weight = 31500.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.078504 restraints weight = 19223.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.078950 restraints weight = 12855.522| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8257 Z= 0.180 Angle : 0.536 5.287 11218 Z= 0.298 Chirality : 0.040 0.123 1322 Planarity : 0.004 0.028 1440 Dihedral : 3.657 15.437 1149 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.12 (0.25), residues: 1094 helix: 2.47 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 0.49 (0.50), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 52 TYR 0.023 0.002 TYR a 145 PHE 0.016 0.001 PHE a 140 TRP 0.010 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 8257) covalent geometry : angle 0.53627 (11218) hydrogen bonds : bond 0.05168 ( 780) hydrogen bonds : angle 4.65168 ( 2331) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 75 MET cc_start: 0.8311 (tmm) cc_final: 0.8080 (tmm) REVERT: O 75 MET cc_start: 0.8142 (tmm) cc_final: 0.7818 (tmm) REVERT: P 63 LEU cc_start: 0.9117 (tp) cc_final: 0.8831 (tp) REVERT: Q 21 MET cc_start: 0.8516 (ppp) cc_final: 0.8101 (ppp) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1454 time to fit residues: 24.5945 Evaluate side-chains 90 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 99 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.081155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.075478 restraints weight = 122030.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.077385 restraints weight = 56897.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.078487 restraints weight = 30203.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.079197 restraints weight = 17990.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.079657 restraints weight = 11790.534| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8257 Z= 0.180 Angle : 0.542 7.153 11218 Z= 0.301 Chirality : 0.040 0.141 1322 Planarity : 0.004 0.028 1440 Dihedral : 3.697 15.528 1149 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.18 (0.25), residues: 1094 helix: 2.59 (0.16), residues: 851 sheet: None (None), residues: 0 loop : 0.34 (0.46), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG a 74 TYR 0.015 0.001 TYR a 145 PHE 0.020 0.001 PHE N 58 TRP 0.011 0.001 TRP a 218 HIS 0.002 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 8257) covalent geometry : angle 0.54239 (11218) hydrogen bonds : bond 0.05058 ( 780) hydrogen bonds : angle 4.55065 ( 2331) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 75 MET cc_start: 0.8284 (tmm) cc_final: 0.8051 (tmm) REVERT: O 21 MET cc_start: 0.7693 (tmm) cc_final: 0.7446 (tmm) REVERT: O 75 MET cc_start: 0.8204 (tmm) cc_final: 0.7899 (tmm) REVERT: P 63 LEU cc_start: 0.9124 (tp) cc_final: 0.8857 (tp) REVERT: Q 21 MET cc_start: 0.8502 (ppp) cc_final: 0.8173 (ppp) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1517 time to fit residues: 25.8429 Evaluate side-chains 88 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 211 GLN ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.080379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.074763 restraints weight = 123135.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.076660 restraints weight = 57131.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.077732 restraints weight = 30152.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.078440 restraints weight = 18054.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.078893 restraints weight = 11817.467| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8257 Z= 0.203 Angle : 0.556 5.812 11218 Z= 0.311 Chirality : 0.040 0.140 1322 Planarity : 0.004 0.030 1440 Dihedral : 3.764 15.358 1149 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.25), residues: 1094 helix: 2.49 (0.16), residues: 869 sheet: None (None), residues: 0 loop : 0.24 (0.49), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 74 TYR 0.015 0.001 TYR a 145 PHE 0.037 0.002 PHE S 58 TRP 0.011 0.002 TRP a 218 HIS 0.003 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 8257) covalent geometry : angle 0.55557 (11218) hydrogen bonds : bond 0.04963 ( 780) hydrogen bonds : angle 4.57326 ( 2331) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 75 MET cc_start: 0.8285 (tmm) cc_final: 0.8032 (tmm) REVERT: O 21 MET cc_start: 0.7768 (tmm) cc_final: 0.7394 (tmm) REVERT: O 75 MET cc_start: 0.8247 (tmm) cc_final: 0.7969 (tmm) REVERT: P 63 LEU cc_start: 0.9126 (tp) cc_final: 0.8777 (tp) REVERT: Q 21 MET cc_start: 0.8450 (ppp) cc_final: 0.8190 (ppp) REVERT: S 75 MET cc_start: 0.8209 (tmm) cc_final: 0.7679 (tmm) REVERT: b 31 PHE cc_start: 0.7780 (t80) cc_final: 0.7343 (t80) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1407 time to fit residues: 24.0329 Evaluate side-chains 88 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 55 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.081315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.075636 restraints weight = 122225.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.077535 restraints weight = 57181.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.078647 restraints weight = 30467.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.079278 restraints weight = 18063.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.079739 restraints weight = 12400.407| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8257 Z= 0.157 Angle : 0.530 6.814 11218 Z= 0.290 Chirality : 0.040 0.121 1322 Planarity : 0.004 0.030 1440 Dihedral : 3.707 15.797 1149 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.34 (0.25), residues: 1094 helix: 2.67 (0.16), residues: 869 sheet: None (None), residues: 0 loop : 0.35 (0.49), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 52 TYR 0.012 0.001 TYR a 145 PHE 0.037 0.002 PHE O 69 TRP 0.011 0.001 TRP a 218 HIS 0.002 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8257) covalent geometry : angle 0.53030 (11218) hydrogen bonds : bond 0.04817 ( 780) hydrogen bonds : angle 4.38357 ( 2331) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 75 MET cc_start: 0.8210 (tmm) cc_final: 0.7937 (tmm) REVERT: O 21 MET cc_start: 0.7757 (tmm) cc_final: 0.7338 (tmm) REVERT: O 75 MET cc_start: 0.8238 (tmm) cc_final: 0.7980 (tmm) REVERT: P 63 LEU cc_start: 0.8969 (tp) cc_final: 0.8684 (tp) REVERT: Q 21 MET cc_start: 0.8328 (ppp) cc_final: 0.7939 (ppp) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1456 time to fit residues: 25.4808 Evaluate side-chains 84 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 93 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.080533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.074892 restraints weight = 122630.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.076779 restraints weight = 57467.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.077872 restraints weight = 30613.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.078552 restraints weight = 18267.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.079010 restraints weight = 12122.370| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8257 Z= 0.192 Angle : 0.542 6.492 11218 Z= 0.303 Chirality : 0.040 0.119 1322 Planarity : 0.004 0.030 1440 Dihedral : 3.726 16.309 1149 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.21 (0.25), residues: 1094 helix: 2.57 (0.16), residues: 872 sheet: None (None), residues: 0 loop : 0.31 (0.48), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 74 TYR 0.015 0.001 TYR a 145 PHE 0.020 0.002 PHE O 69 TRP 0.011 0.002 TRP a 218 HIS 0.002 0.001 HIS a 166 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 8257) covalent geometry : angle 0.54196 (11218) hydrogen bonds : bond 0.04789 ( 780) hydrogen bonds : angle 4.46909 ( 2331) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 75 MET cc_start: 0.8185 (tmm) cc_final: 0.7927 (tmm) REVERT: O 75 MET cc_start: 0.8259 (tmm) cc_final: 0.8003 (tmm) REVERT: P 63 LEU cc_start: 0.9058 (tp) cc_final: 0.8697 (tp) REVERT: Q 21 MET cc_start: 0.8328 (ppp) cc_final: 0.7947 (ppp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1428 time to fit residues: 23.4340 Evaluate side-chains 85 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 96 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.080720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.074987 restraints weight = 123362.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.076884 restraints weight = 57823.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.078019 restraints weight = 30970.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.078726 restraints weight = 18368.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.079197 restraints weight = 12052.403| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8257 Z= 0.168 Angle : 0.523 5.738 11218 Z= 0.288 Chirality : 0.040 0.119 1322 Planarity : 0.004 0.031 1440 Dihedral : 3.700 16.172 1149 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.35 (0.25), residues: 1094 helix: 2.70 (0.16), residues: 869 sheet: None (None), residues: 0 loop : 0.24 (0.48), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 52 TYR 0.016 0.001 TYR a 145 PHE 0.017 0.002 PHE R 74 TRP 0.011 0.001 TRP a 218 HIS 0.002 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 8257) covalent geometry : angle 0.52283 (11218) hydrogen bonds : bond 0.04693 ( 780) hydrogen bonds : angle 4.37288 ( 2331) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 75 MET cc_start: 0.8157 (tmm) cc_final: 0.7909 (tmm) REVERT: O 75 MET cc_start: 0.8277 (tmm) cc_final: 0.8034 (tmm) REVERT: Q 21 MET cc_start: 0.8374 (ppp) cc_final: 0.8021 (ppp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1438 time to fit residues: 23.5996 Evaluate side-chains 86 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 10 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.081337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.075504 restraints weight = 122461.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.077468 restraints weight = 57906.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.078617 restraints weight = 31012.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.079268 restraints weight = 18404.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.079777 restraints weight = 12508.699| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8257 Z= 0.148 Angle : 0.517 5.206 11218 Z= 0.281 Chirality : 0.040 0.126 1322 Planarity : 0.004 0.031 1440 Dihedral : 3.652 15.970 1149 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.52 (0.25), residues: 1094 helix: 2.82 (0.16), residues: 869 sheet: None (None), residues: 0 loop : 0.30 (0.49), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 52 TYR 0.017 0.001 TYR a 145 PHE 0.023 0.001 PHE a 241 TRP 0.012 0.001 TRP a 218 HIS 0.005 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8257) covalent geometry : angle 0.51663 (11218) hydrogen bonds : bond 0.04607 ( 780) hydrogen bonds : angle 4.28282 ( 2331) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 75 MET cc_start: 0.8158 (tmm) cc_final: 0.7899 (tmm) REVERT: O 75 MET cc_start: 0.8261 (tmm) cc_final: 0.8044 (tmm) REVERT: Q 21 MET cc_start: 0.8379 (ppp) cc_final: 0.8078 (ppp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1504 time to fit residues: 24.4496 Evaluate side-chains 85 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 74 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 chunk 81 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 103 optimal weight: 0.4980 chunk 84 optimal weight: 0.5980 chunk 72 optimal weight: 0.0070 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.081952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.076098 restraints weight = 119554.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.078054 restraints weight = 56583.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.079190 restraints weight = 30456.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.079910 restraints weight = 18330.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.080394 restraints weight = 12037.205| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8257 Z= 0.137 Angle : 0.508 6.114 11218 Z= 0.273 Chirality : 0.039 0.152 1322 Planarity : 0.004 0.031 1440 Dihedral : 3.618 15.806 1149 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.69 (0.25), residues: 1094 helix: 2.93 (0.16), residues: 869 sheet: None (None), residues: 0 loop : 0.40 (0.49), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 52 TYR 0.018 0.002 TYR a 145 PHE 0.021 0.001 PHE M 57 TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8257) covalent geometry : angle 0.50849 (11218) hydrogen bonds : bond 0.04488 ( 780) hydrogen bonds : angle 4.20516 ( 2331) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 75 MET cc_start: 0.8177 (tmm) cc_final: 0.7915 (tmm) REVERT: O 21 MET cc_start: 0.7636 (tmm) cc_final: 0.7368 (tmm) REVERT: O 75 MET cc_start: 0.8246 (tmm) cc_final: 0.8022 (tmm) REVERT: Q 21 MET cc_start: 0.8378 (ppp) cc_final: 0.8066 (ppp) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1481 time to fit residues: 23.6699 Evaluate side-chains 81 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 99 optimal weight: 0.0870 chunk 101 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 68 optimal weight: 0.7980 chunk 32 optimal weight: 0.0980 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.082084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.076139 restraints weight = 119399.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.078135 restraints weight = 56664.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.079313 restraints weight = 30430.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.079965 restraints weight = 18109.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.080478 restraints weight = 12408.855| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8257 Z= 0.133 Angle : 0.518 7.913 11218 Z= 0.276 Chirality : 0.039 0.124 1322 Planarity : 0.004 0.030 1440 Dihedral : 3.594 15.685 1149 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.82 (0.25), residues: 1094 helix: 2.99 (0.16), residues: 871 sheet: None (None), residues: 0 loop : 0.58 (0.50), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG T 52 TYR 0.017 0.001 TYR a 145 PHE 0.050 0.001 PHE O 54 TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8257) covalent geometry : angle 0.51771 (11218) hydrogen bonds : bond 0.04448 ( 780) hydrogen bonds : angle 4.15260 ( 2331) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2509.28 seconds wall clock time: 43 minutes 32.81 seconds (2612.81 seconds total)