Starting phenix.real_space_refine on Thu Mar 5 02:27:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nl9_12461/03_2026/7nl9_12461.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nl9_12461/03_2026/7nl9_12461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nl9_12461/03_2026/7nl9_12461.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nl9_12461/03_2026/7nl9_12461.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nl9_12461/03_2026/7nl9_12461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nl9_12461/03_2026/7nl9_12461.map" } resolution = 2.86 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 30 5.16 5 C 6090 2.51 5 N 1513 2.21 5 O 1623 1.98 5 H 9500 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 18756 Number of models: 1 Model: "" Number of chains: 15 Chain: "C" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 137 Classifications: {'peptide': 8} Link IDs: {'PTRANS': 2, 'TRANS': 5} Chain: "G" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 631 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 4, 'TRANS': 37} Chain breaks: 2 Chain: "H" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1562 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain breaks: 3 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: 3.47, per 1000 atoms: 0.19 Number of scatterers: 18756 At special positions: 0 Unit cell: (95.45, 77.19, 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 30 16.00 O 1623 8.00 N 1513 7.00 C 6090 6.00 H 9500 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: 1.87 Conformation dependent library (CDL) restraints added in 552.6 milliseconds 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2186 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 5 sheets defined 80.5% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'G' and resid 53 through 61 Processing helix chain 'G' and resid 227 through 236 removed outlier: 3.520A pdb=" N LEU G 231 " --> pdb=" O ASP G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 96 Processing helix chain 'H' and resid 105 through 118 Processing helix chain 'L' and resid 4 through 46 removed outlier: 3.524A pdb=" N ILE L 8 " --> pdb=" O ASP L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 80 removed outlier: 4.040A pdb=" N THR L 55 " --> pdb=" O GLY L 51 " (cutoff:3.500A) Proline residue: L 56 - end of helix removed outlier: 4.448A pdb=" N ALA L 67 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR L 68 " --> pdb=" O VAL L 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 46 removed outlier: 3.545A pdb=" N ILE M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 80 removed outlier: 4.349A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) Proline residue: M 56 - end of helix removed outlier: 3.524A pdb=" N ILE M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR M 68 " --> pdb=" O VAL M 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 46 Processing helix chain 'N' and resid 49 through 80 removed outlier: 4.563A pdb=" N THR N 55 " --> pdb=" O GLY N 51 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 3.525A pdb=" N ALA N 66 " --> pdb=" O GLY N 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 46 removed outlier: 3.504A pdb=" N ILE O 8 " --> pdb=" O ASP O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 80 removed outlier: 4.699A pdb=" N THR O 55 " --> pdb=" O GLY O 51 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 3.984A pdb=" N ALA O 67 " --> pdb=" O LEU O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 46 removed outlier: 3.732A pdb=" N ILE P 8 " --> pdb=" O ASP P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 81 removed outlier: 3.676A pdb=" N PHE P 54 " --> pdb=" O GLN P 50 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR P 55 " --> pdb=" O GLY P 51 " (cutoff:3.500A) Proline residue: P 56 - end of helix Processing helix chain 'Q' and resid 4 through 46 removed outlier: 3.589A pdb=" N ILE Q 8 " --> pdb=" O ASP Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 50 Processing helix chain 'Q' and resid 51 through 52 No H-bonds generated for 'chain 'Q' and resid 51 through 52' Processing helix chain 'Q' and resid 53 through 80 Processing helix chain 'R' and resid 4 through 46 removed outlier: 3.572A pdb=" N ILE R 8 " --> pdb=" O ASP R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 81 removed outlier: 4.030A pdb=" N THR R 55 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Proline residue: R 56 - end of helix removed outlier: 3.673A pdb=" N ALA R 67 " --> pdb=" O LEU R 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 46 Processing helix chain 'S' and resid 49 through 81 removed outlier: 4.476A pdb=" N THR S 55 " --> pdb=" O GLY S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix Processing helix chain 'T' and resid 4 through 46 removed outlier: 3.644A pdb=" N ILE T 8 " --> pdb=" O ASP T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 81 removed outlier: 4.050A pdb=" N THR T 55 " --> pdb=" O GLY T 51 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 4.192A pdb=" N ALA T 67 " --> pdb=" O LEU T 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 51 Processing helix chain 'a' and resid 60 through 81 Processing helix chain 'a' and resid 88 through 106 removed outlier: 3.571A 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 154 removed outlier: 3.501A pdb=" N VAL a 134 " --> pdb=" O ASP a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 165 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 Proline residue: a 182 - end of helix removed outlier: 3.866A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY a 196 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA a 201 " --> pdb=" O GLY a 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 207 through 245 removed outlier: 5.760A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.778A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 49 removed outlier: 3.624A pdb=" N VAL b 49 " --> pdb=" O ILE b 45 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 84 removed outlier: 3.563A pdb=" N ALA b 79 " --> pdb=" O ALA b 75 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLN b 82 " --> pdb=" O VAL b 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 22 Processing helix chain 'd' and resid 22 through 61 Processing sheet with id=AA1, first strand: chain 'C' and resid 539 through 540 Processing sheet with id=AA2, first strand: chain 'G' and resid 223 through 224 removed outlier: 6.379A pdb=" N SER G 223 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N GLN H 44 " --> pdb=" O SER G 223 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASN H 5 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE H 79 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLU H 7 " --> pdb=" O ILE H 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 31 through 34 removed outlier: 4.168A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=AA5, first strand: chain 'a' and resid 112 through 114 840 hydrogen bonds defined for protein. 2496 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: 5.09 Time building geometry restraints manager: 2.53 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: 9499 1.03 - 1.23: 2 1.23 - 1.42: 3828 1.42 - 1.61: 5551 1.61 - 1.81: 59 Bond restraints: 18939 Sorted by residual: bond pdb=" CA VAL d 23 " pdb=" CB VAL d 23 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 7.72e-01 bond pdb=" N GLN L 46 " pdb=" CA GLN L 46 " ideal model delta sigma weight residual 1.463 1.455 0.008 9.30e-03 1.16e+04 7.49e-01 bond pdb=" CB MET T 21 " pdb=" CG MET T 21 " ideal model delta sigma weight residual 1.520 1.500 0.020 3.00e-02 1.11e+03 4.42e-01 bond pdb=" CB ASN R 71 " pdb=" CG ASN R 71 " ideal model delta sigma weight residual 1.516 1.501 0.015 2.50e-02 1.60e+03 3.64e-01 bond pdb=" C GLN R 46 " pdb=" O GLN R 46 " ideal model delta sigma weight residual 1.249 1.244 0.005 8.50e-03 1.38e+04 3.61e-01 ... (remaining 18934 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 32348 1.04 - 2.08: 1901 2.08 - 3.12: 60 3.12 - 4.16: 51 4.16 - 5.20: 9 Bond angle restraints: 34369 Sorted by residual: angle pdb=" C CYS a 144 " pdb=" N TYR a 145 " pdb=" CA TYR a 145 " ideal model delta sigma weight residual 121.14 115.94 5.20 1.75e+00 3.27e-01 8.83e+00 angle pdb=" CA TYR a 145 " pdb=" CB TYR a 145 " pdb=" CG TYR a 145 " ideal model delta sigma weight residual 113.90 118.74 -4.84 1.80e+00 3.09e-01 7.24e+00 angle pdb=" N TYR a 145 " pdb=" CA TYR a 145 " pdb=" CB TYR a 145 " ideal model delta sigma weight residual 110.40 113.94 -3.54 1.63e+00 3.76e-01 4.73e+00 angle pdb=" N GLY Q 62 " pdb=" CA GLY Q 62 " pdb=" C GLY Q 62 " ideal model delta sigma weight residual 113.18 109.19 3.99 2.37e+00 1.78e-01 2.83e+00 angle pdb=" C LEU b 39 " pdb=" N ILE b 40 " pdb=" CA ILE b 40 " ideal model delta sigma weight residual 120.46 118.24 2.22 1.37e+00 5.33e-01 2.62e+00 ... (remaining 34364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 7661 16.70 - 33.40: 733 33.40 - 50.10: 206 50.10 - 66.80: 242 66.80 - 83.50: 3 Dihedral angle restraints: 8845 sinusoidal: 4753 harmonic: 4092 Sorted by residual: dihedral pdb=" CA GLU G 225 " pdb=" C GLU G 225 " pdb=" N PRO G 226 " pdb=" CA PRO G 226 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA GLN L 46 " pdb=" C GLN L 46 " pdb=" N PRO L 47 " pdb=" CA PRO L 47 " ideal model delta harmonic sigma weight residual 180.00 -164.70 -15.30 0 5.00e+00 4.00e-02 9.36e+00 dihedral pdb=" N ARG H 78 " pdb=" CA ARG H 78 " pdb=" CB ARG H 78 " pdb=" CG ARG H 78 " ideal model delta sinusoidal sigma weight residual -60.00 -113.95 53.95 3 1.50e+01 4.44e-03 9.25e+00 ... (remaining 8842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 956 0.029 - 0.059: 311 0.059 - 0.088: 192 0.088 - 0.117: 50 0.117 - 0.146: 6 Chirality restraints: 1515 Sorted by residual: chirality pdb=" CA PRO H 36 " pdb=" N PRO H 36 " pdb=" C PRO H 36 " pdb=" CB PRO H 36 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA VAL H 77 " pdb=" N VAL H 77 " pdb=" C VAL H 77 " pdb=" CB VAL H 77 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA ILE a 81 " pdb=" N ILE a 81 " pdb=" C ILE a 81 " pdb=" CB ILE a 81 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 1512 not shown) Planarity restraints: 2834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 35 " 0.031 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO H 36 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO H 36 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 36 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 52 " 0.142 9.50e-02 1.11e+02 4.74e-02 2.51e+00 pdb=" NE ARG R 52 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG R 52 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG R 52 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG R 52 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG R 52 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG R 52 " 0.003 2.00e-02 2.50e+03 pdb="HH21 ARG R 52 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG R 52 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Q 66 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.33e+00 pdb=" C ALA Q 66 " -0.026 2.00e-02 2.50e+03 pdb=" O ALA Q 66 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA Q 67 " 0.009 2.00e-02 2.50e+03 ... (remaining 2831 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1310 2.22 - 2.81: 40705 2.81 - 3.41: 55678 3.41 - 4.00: 73369 4.00 - 4.60: 114251 Nonbonded interactions: 285313 Sorted by model distance: nonbonded pdb=" OE1 GLU N 48 " pdb=" H GLU N 48 " model vdw 1.619 2.450 nonbonded pdb=" OE2 GLU G 225 " pdb="HH22 ARG L 45 " model vdw 1.656 2.450 nonbonded pdb="HE22 GLN O 86 " pdb=" OD2 ASP P 4 " model vdw 1.657 2.450 nonbonded pdb=" O ASN O 6 " pdb=" HG1 THR O 10 " model vdw 1.682 2.450 nonbonded pdb=" OE1 GLU O 48 " pdb=" H GLU O 48 " model vdw 1.689 2.450 ... (remaining 285308 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 individual isotropic 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: 8.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.900 Find NCS groups from input model: 0.180 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:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 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 0.024 9439 Z= 0.132 Angle : 0.475 5.200 12819 Z= 0.261 Chirality : 0.039 0.146 1515 Planarity : 0.005 0.062 1645 Dihedral : 13.117 83.497 3218 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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: 1.60 (0.25), residues: 1229 helix: 1.24 (0.17), residues: 980 sheet: -0.83 (0.82), residues: 32 loop : 0.98 (0.45), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 52 TYR 0.011 0.001 TYR a 145 PHE 0.018 0.001 PHE L 69 TRP 0.013 0.001 TRP a 218 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9439) covalent geometry : angle 0.47451 (12819) hydrogen bonds : bond 0.13798 ( 840) hydrogen bonds : angle 6.69818 ( 2496) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: H 47 ASP cc_start: 0.8184 (m-30) cc_final: 0.7869 (m-30) REVERT: M 46 GLN cc_start: 0.8081 (mp10) cc_final: 0.7865 (mp10) outliers start: 0 outliers final: 1 residues processed: 131 average time/residue: 1.2472 time to fit residues: 175.2014 Evaluate side-chains 87 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 90 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.079370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.064255 restraints weight = 53606.706| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.93 r_work: 0.2826 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9439 Z= 0.217 Angle : 0.541 6.283 12819 Z= 0.298 Chirality : 0.040 0.172 1515 Planarity : 0.005 0.054 1645 Dihedral : 3.926 25.349 1307 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.56 % Allowed : 9.04 % Favored : 89.40 % 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: 2.65 (0.24), residues: 1229 helix: 2.05 (0.16), residues: 987 sheet: -0.87 (0.85), residues: 34 loop : 0.97 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 55 TYR 0.029 0.001 TYR a 145 PHE 0.014 0.002 PHE a 142 TRP 0.012 0.001 TRP a 218 HIS 0.004 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 9439) covalent geometry : angle 0.54141 (12819) hydrogen bonds : bond 0.05400 ( 840) hydrogen bonds : angle 4.36134 ( 2496) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 105 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.7035 (mtt-85) REVERT: M 46 GLN cc_start: 0.8433 (mp10) cc_final: 0.8169 (mp10) REVERT: d 33 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.7206 (tt0) outliers start: 14 outliers final: 5 residues processed: 100 average time/residue: 1.2686 time to fit residues: 136.0138 Evaluate side-chains 91 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain Q residue 86 GLN Chi-restraints excluded: chain S residue 86 GLN Chi-restraints excluded: chain d residue 33 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 98 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 68 optimal weight: 0.1980 chunk 119 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.079616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.064546 restraints weight = 53558.691| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.93 r_work: 0.2818 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9439 Z= 0.185 Angle : 0.511 5.122 12819 Z= 0.278 Chirality : 0.040 0.165 1515 Planarity : 0.004 0.051 1645 Dihedral : 3.994 25.608 1307 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.56 % Allowed : 9.71 % Favored : 88.73 % 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: 3.07 (0.24), residues: 1229 helix: 2.39 (0.16), residues: 987 sheet: -0.96 (0.83), residues: 34 loop : 0.91 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 52 TYR 0.026 0.001 TYR a 145 PHE 0.014 0.001 PHE M 58 TRP 0.012 0.001 TRP a 218 HIS 0.004 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9439) covalent geometry : angle 0.51147 (12819) hydrogen bonds : bond 0.04967 ( 840) hydrogen bonds : angle 4.10953 ( 2496) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 105 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.7062 (mtt-85) REVERT: M 46 GLN cc_start: 0.8481 (mp10) cc_final: 0.8144 (mp10) REVERT: M 65 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8092 (mm-30) REVERT: Q 75 MET cc_start: 0.9094 (ttp) cc_final: 0.8887 (ttp) outliers start: 14 outliers final: 9 residues processed: 94 average time/residue: 1.2948 time to fit residues: 130.1426 Evaluate side-chains 94 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain P residue 21 MET Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain S residue 86 GLN Chi-restraints excluded: chain a residue 246 GLU Chi-restraints excluded: chain b residue 25 LEU Chi-restraints excluded: chain d residue 35 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 44 optimal weight: 0.0870 chunk 46 optimal weight: 0.7980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 GLN ** a 192 ASN ** 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 = 0.3201 r_free = 0.3201 target = 0.079094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.064018 restraints weight = 53690.209| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.93 r_work: 0.2818 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9439 Z= 0.183 Angle : 0.509 6.677 12819 Z= 0.276 Chirality : 0.039 0.165 1515 Planarity : 0.004 0.050 1645 Dihedral : 3.933 17.152 1305 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.90 % Allowed : 10.60 % Favored : 87.50 % 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: 3.29 (0.24), residues: 1229 helix: 2.57 (0.16), residues: 987 sheet: -1.20 (0.80), residues: 34 loop : 0.91 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 52 TYR 0.024 0.001 TYR a 145 PHE 0.016 0.001 PHE M 58 TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9439) covalent geometry : angle 0.50949 (12819) hydrogen bonds : bond 0.04782 ( 840) hydrogen bonds : angle 3.99284 ( 2496) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 105 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.7068 (mtt-85) REVERT: M 65 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8033 (mm-30) REVERT: d 33 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7333 (mt0) REVERT: d 43 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7726 (mm-30) outliers start: 17 outliers final: 10 residues processed: 92 average time/residue: 1.3905 time to fit residues: 136.6005 Evaluate side-chains 94 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain P residue 21 MET Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain Q residue 86 GLN Chi-restraints excluded: chain S residue 86 GLN Chi-restraints excluded: chain a residue 246 GLU Chi-restraints excluded: chain b residue 25 LEU Chi-restraints excluded: chain d residue 33 GLN Chi-restraints excluded: chain d residue 35 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 54 optimal weight: 0.0070 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 GLN ** a 192 ASN ** 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 = 0.3217 r_free = 0.3217 target = 0.080099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.065103 restraints weight = 53054.192| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.93 r_work: 0.2831 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9439 Z= 0.144 Angle : 0.485 4.942 12819 Z= 0.261 Chirality : 0.039 0.152 1515 Planarity : 0.004 0.047 1645 Dihedral : 3.872 17.121 1305 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.67 % Allowed : 11.83 % Favored : 86.50 % 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: 3.49 (0.24), residues: 1229 helix: 2.73 (0.16), residues: 985 sheet: -1.15 (0.81), residues: 34 loop : 0.92 (0.46), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 52 TYR 0.021 0.001 TYR a 145 PHE 0.015 0.001 PHE M 58 TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9439) covalent geometry : angle 0.48545 (12819) hydrogen bonds : bond 0.04583 ( 840) hydrogen bonds : angle 3.91214 ( 2496) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 105 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.7106 (mtt-85) REVERT: M 65 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8025 (mm-30) REVERT: Q 86 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6976 (pp30) outliers start: 15 outliers final: 9 residues processed: 92 average time/residue: 1.4245 time to fit residues: 140.0746 Evaluate side-chains 92 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain P residue 21 MET Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain Q residue 86 GLN Chi-restraints excluded: chain S residue 86 GLN Chi-restraints excluded: chain a residue 246 GLU Chi-restraints excluded: chain b residue 25 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 35 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 6 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 44 optimal weight: 0.0870 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 GLN ** a 192 ASN ** 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 = 0.3209 r_free = 0.3209 target = 0.079550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.064449 restraints weight = 53438.512| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.93 r_work: 0.2824 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9439 Z= 0.170 Angle : 0.503 6.892 12819 Z= 0.270 Chirality : 0.039 0.161 1515 Planarity : 0.004 0.048 1645 Dihedral : 3.903 18.891 1305 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.67 % Allowed : 12.05 % Favored : 86.27 % 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: 3.48 (0.24), residues: 1229 helix: 2.73 (0.16), residues: 987 sheet: -1.18 (0.80), residues: 34 loop : 0.84 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 52 TYR 0.021 0.001 TYR a 145 PHE 0.015 0.001 PHE M 58 TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 9439) covalent geometry : angle 0.50280 (12819) hydrogen bonds : bond 0.04620 ( 840) hydrogen bonds : angle 3.89200 ( 2496) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 105 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.7104 (mtt-85) outliers start: 15 outliers final: 10 residues processed: 91 average time/residue: 1.3642 time to fit residues: 132.5572 Evaluate side-chains 88 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain P residue 21 MET Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain S residue 86 GLN Chi-restraints excluded: chain a residue 246 GLU Chi-restraints excluded: chain b residue 25 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 35 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 0.0670 chunk 110 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.079450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.064354 restraints weight = 53573.983| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.94 r_work: 0.2821 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9439 Z= 0.169 Angle : 0.496 4.987 12819 Z= 0.267 Chirality : 0.039 0.162 1515 Planarity : 0.004 0.048 1645 Dihedral : 3.886 16.476 1305 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.67 % Allowed : 12.61 % Favored : 85.71 % 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: 3.50 (0.24), residues: 1229 helix: 2.74 (0.16), residues: 987 sheet: -1.14 (0.81), residues: 34 loop : 0.86 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 55 TYR 0.020 0.001 TYR a 145 PHE 0.014 0.001 PHE M 58 TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9439) covalent geometry : angle 0.49577 (12819) hydrogen bonds : bond 0.04604 ( 840) hydrogen bonds : angle 3.87652 ( 2496) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 58 GLU cc_start: 0.6957 (mp0) cc_final: 0.6751 (mp0) REVERT: H 105 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.7097 (mtt-85) REVERT: M 65 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8050 (mm-30) outliers start: 15 outliers final: 8 residues processed: 90 average time/residue: 1.3067 time to fit residues: 126.3285 Evaluate side-chains 90 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain P residue 21 MET Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain S residue 86 GLN Chi-restraints excluded: chain b residue 25 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 35 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 49 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 83 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.079121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.064133 restraints weight = 53841.789| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.93 r_work: 0.2816 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9439 Z= 0.190 Angle : 0.520 7.596 12819 Z= 0.281 Chirality : 0.039 0.168 1515 Planarity : 0.004 0.050 1645 Dihedral : 3.908 16.261 1305 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.56 % Allowed : 13.06 % Favored : 85.38 % 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: 3.45 (0.24), residues: 1229 helix: 2.70 (0.16), residues: 987 sheet: -1.17 (0.80), residues: 34 loop : 0.88 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 52 TYR 0.020 0.001 TYR a 145 PHE 0.015 0.001 PHE a 142 TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 9439) covalent geometry : angle 0.51982 (12819) hydrogen bonds : bond 0.04689 ( 840) hydrogen bonds : angle 3.88982 ( 2496) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 105 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.7019 (mtt-85) REVERT: b 73 LYS cc_start: 0.8171 (tppt) cc_final: 0.7935 (tppp) outliers start: 14 outliers final: 8 residues processed: 89 average time/residue: 1.2491 time to fit residues: 119.6728 Evaluate side-chains 87 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain P residue 21 MET Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain S residue 86 GLN Chi-restraints excluded: chain b residue 25 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 35 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 74 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.0870 chunk 116 optimal weight: 0.0870 chunk 22 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 44 optimal weight: 0.2980 chunk 64 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 81 optimal weight: 0.9980 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.080938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.065997 restraints weight = 52956.019| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.93 r_work: 0.2857 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9439 Z= 0.122 Angle : 0.483 5.215 12819 Z= 0.257 Chirality : 0.039 0.137 1515 Planarity : 0.004 0.046 1645 Dihedral : 3.788 16.903 1305 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.00 % Allowed : 13.39 % Favored : 85.60 % 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: 3.75 (0.24), residues: 1229 helix: 2.91 (0.16), residues: 985 sheet: -1.17 (0.79), residues: 32 loop : 0.93 (0.46), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 52 TYR 0.020 0.001 TYR a 145 PHE 0.016 0.001 PHE M 58 TRP 0.013 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 9439) covalent geometry : angle 0.48277 (12819) hydrogen bonds : bond 0.04292 ( 840) hydrogen bonds : angle 3.79775 ( 2496) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 105 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.7063 (mtt-85) REVERT: M 32 ASP cc_start: 0.8920 (m-30) cc_final: 0.8534 (m-30) REVERT: M 65 GLU cc_start: 0.8442 (mm-30) cc_final: 0.7954 (mm-30) REVERT: b 73 LYS cc_start: 0.8142 (tppt) cc_final: 0.7911 (tppp) outliers start: 9 outliers final: 4 residues processed: 89 average time/residue: 1.2887 time to fit residues: 123.1510 Evaluate side-chains 85 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain P residue 21 MET Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain b residue 25 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 79 optimal weight: 0.0870 chunk 13 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3222 r_free = 0.3222 target = 0.080280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.065392 restraints weight = 53475.771| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.93 r_work: 0.2842 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9439 Z= 0.151 Angle : 0.498 7.863 12819 Z= 0.267 Chirality : 0.039 0.155 1515 Planarity : 0.004 0.047 1645 Dihedral : 3.774 16.218 1305 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.67 % Allowed : 14.06 % Favored : 85.27 % 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: 3.75 (0.24), residues: 1229 helix: 2.90 (0.16), residues: 985 sheet: -1.00 (0.81), residues: 34 loop : 1.04 (0.46), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 52 TYR 0.020 0.001 TYR a 145 PHE 0.014 0.001 PHE M 58 TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9439) covalent geometry : angle 0.49813 (12819) hydrogen bonds : bond 0.04410 ( 840) hydrogen bonds : angle 3.79103 ( 2496) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 105 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.7047 (mtt-85) REVERT: M 65 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7922 (mm-30) REVERT: Q 75 MET cc_start: 0.8934 (ttp) cc_final: 0.8516 (ttt) REVERT: b 73 LYS cc_start: 0.8143 (tppt) cc_final: 0.7687 (tppp) outliers start: 6 outliers final: 4 residues processed: 85 average time/residue: 1.2078 time to fit residues: 110.0324 Evaluate side-chains 84 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain P residue 21 MET Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain b residue 25 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3207 r_free = 0.3207 target = 0.079505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.064559 restraints weight = 53656.859| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.93 r_work: 0.2823 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9439 Z= 0.181 Angle : 0.507 5.673 12819 Z= 0.273 Chirality : 0.039 0.166 1515 Planarity : 0.004 0.048 1645 Dihedral : 3.837 16.019 1305 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.89 % Allowed : 13.62 % Favored : 85.49 % 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: 3.62 (0.24), residues: 1229 helix: 2.81 (0.16), residues: 987 sheet: -0.98 (0.82), residues: 34 loop : 0.92 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 45 TYR 0.019 0.001 TYR a 145 PHE 0.015 0.001 PHE a 142 TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 9439) covalent geometry : angle 0.50736 (12819) hydrogen bonds : bond 0.04576 ( 840) hydrogen bonds : angle 3.82846 ( 2496) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5551.71 seconds wall clock time: 94 minutes 47.53 seconds (5687.53 seconds total)