Starting phenix.real_space_refine on Fri Jul 3 05:05:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vmj_43358/07_2026/8vmj_43358.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vmj_43358/07_2026/8vmj_43358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vmj_43358/07_2026/8vmj_43358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vmj_43358/07_2026/8vmj_43358.map" model { file = "/net/cci-nas-00/data/ceres_data/8vmj_43358/07_2026/8vmj_43358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vmj_43358/07_2026/8vmj_43358.cif" } resolution = 3.1 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= 0.002 sd= 0.060 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 P 314 5.49 5 S 14 5.16 5 C 6889 2.51 5 N 2355 2.21 5 O 2968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12540 Number of models: 1 Model: "" Number of chains: 10 Chain: "H" Number of atoms: 3237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3237 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Chain: "I" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "J" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "K" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 736 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "O" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "Q" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 667 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "R" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "S" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 3202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3202 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Time building chain proxies: 2.65, per 1000 atoms: 0.21 Number of scatterers: 12540 At special positions: 0 Unit cell: (106.05, 141.75, 121.8, 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 14 16.00 P 314 15.00 O 2968 8.00 N 2355 7.00 C 6889 6.00 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: 1.26 Conformation dependent library (CDL) restraints added in 405.4 milliseconds 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 69.7% alpha, 2.6% beta 157 base pairs and 269 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'I' and resid 45 through 57 Processing helix chain 'I' and resid 63 through 77 removed outlier: 3.898A pdb=" N ASP I 77 " --> pdb=" O GLU I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 114 removed outlier: 3.614A pdb=" N MET I 90 " --> pdb=" O SER I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 132 Processing helix chain 'J' and resid 30 through 42 Processing helix chain 'J' and resid 49 through 76 removed outlier: 3.554A pdb=" N GLU J 53 " --> pdb=" O LEU J 49 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG J 55 " --> pdb=" O TYR J 51 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP J 68 " --> pdb=" O ASN J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 94 Processing helix chain 'K' and resid 16 through 21 removed outlier: 3.559A pdb=" N ARG K 20 " --> pdb=" O THR K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 37 Processing helix chain 'K' and resid 45 through 73 removed outlier: 4.348A pdb=" N VAL K 49 " --> pdb=" O ALA K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 90 removed outlier: 3.660A pdb=" N ASP K 90 " --> pdb=" O ALA K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 97 removed outlier: 3.521A pdb=" N LEU K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 46 Processing helix chain 'M' and resid 52 through 81 removed outlier: 3.503A pdb=" N ASN M 81 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 99 Processing helix chain 'M' and resid 101 through 121 removed outlier: 3.742A pdb=" N SER M 109 " --> pdb=" O LYS M 105 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA M 121 " --> pdb=" O LYS M 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 57 Processing helix chain 'O' and resid 63 through 75 Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 131 Processing helix chain 'Q' and resid 25 through 29 Processing helix chain 'Q' and resid 30 through 42 Processing helix chain 'Q' and resid 49 through 77 removed outlier: 4.098A pdb=" N GLU Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP Q 68 " --> pdb=" O ASN Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 93 Processing helix chain 'R' and resid 16 through 22 removed outlier: 3.831A pdb=" N ARG R 20 " --> pdb=" O THR R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 37 Processing helix chain 'R' and resid 46 through 73 Processing helix chain 'R' and resid 79 through 90 removed outlier: 3.543A pdb=" N ASP R 90 " --> pdb=" O ALA R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 97 Processing helix chain 'S' and resid 34 through 46 Processing helix chain 'S' and resid 52 through 81 Processing helix chain 'S' and resid 87 through 99 Processing helix chain 'S' and resid 101 through 121 removed outlier: 3.617A pdb=" N LYS S 105 " --> pdb=" O GLY S 101 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA S 121 " --> pdb=" O LYS S 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 83 through 84 removed outlier: 7.168A pdb=" N ARG I 83 " --> pdb=" O VAL J 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'I' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'J' and resid 96 through 98 removed outlier: 6.151A pdb=" N THR J 96 " --> pdb=" O THR R 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'K' and resid 42 through 43 removed outlier: 7.369A pdb=" N ARG K 42 " --> pdb=" O ILE M 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'K' and resid 100 through 102 removed outlier: 6.928A pdb=" N THR K 101 " --> pdb=" O TYR Q 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.754A pdb=" N ARG O 83 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'R' and resid 42 through 43 removed outlier: 7.383A pdb=" N ARG R 42 " --> pdb=" O ILE S 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'R' and resid 77 through 78 394 hydrogen bonds defined for protein. 1176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 398 hydrogen bonds 756 hydrogen bond angles 0 basepair planarities 157 basepair parallelities 269 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1728 1.33 - 1.45: 4924 1.45 - 1.57: 6098 1.57 - 1.69: 629 1.69 - 1.82: 24 Bond restraints: 13403 Sorted by residual: bond pdb=" CG PRO O 38 " pdb=" CD PRO O 38 " ideal model delta sigma weight residual 1.503 1.205 0.298 3.40e-02 8.65e+02 7.70e+01 bond pdb=" N PRO O 38 " pdb=" CD PRO O 38 " ideal model delta sigma weight residual 1.473 1.558 -0.085 1.40e-02 5.10e+03 3.71e+01 bond pdb=" C3' DG D 4 " pdb=" C2' DG D 4 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DC D 103 " pdb=" C2' DC D 103 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DG D 82 " pdb=" C2' DG D 82 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 ... (remaining 13398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 19392 3.79 - 7.58: 61 7.58 - 11.37: 1 11.37 - 15.16: 4 15.16 - 18.95: 1 Bond angle restraints: 19459 Sorted by residual: angle pdb=" CA PRO O 38 " pdb=" N PRO O 38 " pdb=" CD PRO O 38 " ideal model delta sigma weight residual 112.00 93.05 18.95 1.40e+00 5.10e-01 1.83e+02 angle pdb=" N PRO O 38 " pdb=" CD PRO O 38 " pdb=" CG PRO O 38 " ideal model delta sigma weight residual 103.20 88.45 14.75 1.50e+00 4.44e-01 9.67e+01 angle pdb=" CA PRO I 43 " pdb=" N PRO I 43 " pdb=" CD PRO I 43 " ideal model delta sigma weight residual 112.00 98.62 13.38 1.40e+00 5.10e-01 9.13e+01 angle pdb=" CA PRO O 38 " pdb=" CB PRO O 38 " pdb=" CG PRO O 38 " ideal model delta sigma weight residual 104.50 91.98 12.52 1.90e+00 2.77e-01 4.34e+01 angle pdb=" N3 DT D 140 " pdb=" C4 DT D 140 " pdb=" O4 DT D 140 " ideal model delta sigma weight residual 119.90 122.69 -2.79 6.00e-01 2.78e+00 2.17e+01 ... (remaining 19454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 5729 35.91 - 71.82: 1433 71.82 - 107.73: 28 107.73 - 143.65: 8 143.65 - 179.56: 24 Dihedral angle restraints: 7222 sinusoidal: 4972 harmonic: 2250 Sorted by residual: dihedral pdb=" CA PHE R 25 " pdb=" C PHE R 25 " pdb=" N PRO R 26 " pdb=" CA PRO R 26 " ideal model delta harmonic sigma weight residual -180.00 -159.37 -20.63 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA HIS S 79 " pdb=" C HIS S 79 " pdb=" N TYR S 80 " pdb=" CA TYR S 80 " ideal model delta harmonic sigma weight residual -180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C4' DT D 68 " pdb=" C3' DT D 68 " pdb=" O3' DT D 68 " pdb=" P DT D 69 " ideal model delta sinusoidal sigma weight residual 220.00 40.44 179.56 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 7219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1589 0.049 - 0.098: 502 0.098 - 0.146: 109 0.146 - 0.195: 16 0.195 - 0.244: 2 Chirality restraints: 2218 Sorted by residual: chirality pdb=" CB THR S 112 " pdb=" CA THR S 112 " pdb=" OG1 THR S 112 " pdb=" CG2 THR S 112 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" C3' DC D 92 " pdb=" C4' DC D 92 " pdb=" O3' DC D 92 " pdb=" C2' DC D 92 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C3' DC D 28 " pdb=" C4' DC D 28 " pdb=" O3' DC D 28 " pdb=" C2' DC D 28 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.20e-01 ... (remaining 2215 not shown) Planarity restraints: 1377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG I 42 " 0.116 5.00e-02 4.00e+02 1.64e-01 4.29e+01 pdb=" N PRO I 43 " -0.283 5.00e-02 4.00e+02 pdb=" CA PRO I 43 " 0.083 5.00e-02 4.00e+02 pdb=" CD PRO I 43 " 0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS O 37 " 0.082 5.00e-02 4.00e+02 1.09e-01 1.90e+01 pdb=" N PRO O 38 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO O 38 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO O 38 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 80 " 0.031 2.00e-02 2.50e+03 2.66e-02 1.42e+01 pdb=" CG TYR S 80 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR S 80 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR S 80 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR S 80 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR S 80 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR S 80 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR S 80 " 0.001 2.00e-02 2.50e+03 ... (remaining 1374 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 268 2.65 - 3.21: 10562 3.21 - 3.77: 24047 3.77 - 4.34: 30514 4.34 - 4.90: 43251 Nonbonded interactions: 108642 Sorted by model distance: nonbonded pdb=" O2 DC H 110 " pdb=" N2 DG D 48 " model vdw 2.082 2.496 nonbonded pdb=" N2 DG H 137 " pdb=" O2 DC D 21 " model vdw 2.097 2.496 nonbonded pdb=" OD2 ASP M 65 " pdb=" OH TYR Q 98 " model vdw 2.101 3.040 nonbonded pdb=" N2 DG H 94 " pdb=" O2 DC D 64 " model vdw 2.110 2.496 nonbonded pdb=" O2 DC H 154 " pdb=" N2 DG D 4 " model vdw 2.125 2.496 ... (remaining 108637 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 'I' and resid 37 through 135) selection = chain 'O' } ncs_group { reference = (chain 'J' and ((resid 20 through 23 and (name N or name CA or name C or name O \ or name CB )) or resid 24 through 102)) selection = (chain 'Q' and resid 20 through 102) } ncs_group { reference = chain 'K' selection = (chain 'R' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 119)) } ncs_group { reference = chain 'M' selection = (chain 'S' and resid 28 through 122) } 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: 5.390 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: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.140 Find NCS groups from input model: 0.160 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 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 : 0.007 0.298 13403 Z= 0.556 Angle : 0.886 18.945 19459 Z= 0.732 Chirality : 0.050 0.244 2218 Planarity : 0.008 0.164 1377 Dihedral : 31.124 179.557 5770 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.63 % Allowed : 23.58 % Favored : 75.79 % 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: 0.60 (0.30), residues: 760 helix: 1.06 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.11 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 40 TYR 0.064 0.003 TYR S 80 PHE 0.022 0.003 PHE R 25 HIS 0.011 0.002 HIS R 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00711 / 0.56 (13403) covalent geometry : angle 0.88635 / 0.73 (19459) hydrogen bonds : bond 0.10030 / 11.12 ( 792) hydrogen bonds : angle 4.07596 / 5.32 ( 1932) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: S 102 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7220 (tm-30) outliers start: 4 outliers final: 3 residues processed: 129 average time/residue: 0.1559 time to fit residues: 27.0864 Evaluate side-chains 124 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 121 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain R residue 25 PHE Chi-restraints excluded: chain S residue 49 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.0070 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 60 ASN ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 GLN O 125 GLN R 110 ASN S 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.186879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.140756 restraints weight = 20873.285| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 1.55 r_work: 0.3770 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 13403 Z= 0.180 Angle : 0.705 7.929 19459 Z= 0.414 Chirality : 0.051 0.351 2218 Planarity : 0.005 0.067 1377 Dihedral : 33.808 177.033 4275 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.59 % Allowed : 20.57 % Favored : 74.84 % 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: 1.05 (0.30), residues: 760 helix: 1.42 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -1.06 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 71 TYR 0.044 0.002 TYR S 80 PHE 0.014 0.002 PHE I 67 HIS 0.003 0.001 HIS S 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.18 (13403) covalent geometry : angle 0.70503 / 0.41 (19459) hydrogen bonds : bond 0.07966 / 8.83 ( 792) hydrogen bonds : angle 3.43382 / 4.50 ( 1932) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: K 25 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7650 (t80) REVERT: M 48 ASP cc_start: 0.8206 (p0) cc_final: 0.7960 (p0) REVERT: O 59 GLU cc_start: 0.7555 (pp20) cc_final: 0.7264 (pp20) REVERT: Q 77 LYS cc_start: 0.7863 (mmmt) cc_final: 0.7650 (mmmt) outliers start: 29 outliers final: 19 residues processed: 152 average time/residue: 0.1557 time to fit residues: 31.6320 Evaluate side-chains 146 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 90 MET Chi-restraints excluded: chain Q residue 47 SER Chi-restraints excluded: chain R residue 24 GLN Chi-restraints excluded: chain R residue 25 PHE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 97 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 38 ASN M 81 ASN O 108 ASN ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 GLN R 110 ASN S 79 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.174970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.127458 restraints weight = 20545.301| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.52 r_work: 0.3587 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13403 Z= 0.252 Angle : 0.841 12.218 19459 Z= 0.471 Chirality : 0.057 0.398 2218 Planarity : 0.007 0.050 1377 Dihedral : 33.979 179.286 4273 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 7.59 % Allowed : 18.35 % Favored : 74.05 % 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: 0.35 (0.29), residues: 760 helix: 0.89 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -1.29 (0.38), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG R 32 TYR 0.065 0.003 TYR S 80 PHE 0.021 0.004 PHE O 104 HIS 0.010 0.002 HIS O 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.25 (13403) covalent geometry : angle 0.84124 / 0.47 (19459) hydrogen bonds : bond 0.08975 / 10.06 ( 792) hydrogen bonds : angle 3.67315 / 4.75 ( 1932) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 140 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 60 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8939 (mm) REVERT: J 91 LYS cc_start: 0.9000 (ttpp) cc_final: 0.8650 (ttpp) REVERT: K 25 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.7712 (t80) REVERT: M 48 ASP cc_start: 0.8343 (p0) cc_final: 0.8130 (p0) REVERT: M 96 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7650 (mpp80) REVERT: M 106 HIS cc_start: 0.8405 (OUTLIER) cc_final: 0.8199 (m170) REVERT: O 97 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7978 (mt-10) REVERT: Q 77 LYS cc_start: 0.8058 (mmmt) cc_final: 0.7793 (mmmt) REVERT: R 74 LYS cc_start: 0.8555 (mmtt) cc_final: 0.8321 (mmtt) REVERT: S 119 THR cc_start: 0.8358 (m) cc_final: 0.8137 (p) outliers start: 48 outliers final: 32 residues processed: 170 average time/residue: 0.1527 time to fit residues: 34.8267 Evaluate side-chains 157 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 89 ARG Chi-restraints excluded: chain M residue 96 ARG Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 106 HIS Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 85 GLN Chi-restraints excluded: chain O residue 90 MET Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 91 LYS Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 24 GLN Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 106 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 10 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 60 optimal weight: 0.0970 chunk 51 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 100 optimal weight: 8.9990 chunk 21 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 GLN ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** 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 = 0.4411 r_free = 0.4411 target = 0.176532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.129860 restraints weight = 20254.242| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.51 r_work: 0.3631 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13403 Z= 0.170 Angle : 0.702 8.240 19459 Z= 0.405 Chirality : 0.051 0.339 2218 Planarity : 0.004 0.041 1377 Dihedral : 34.003 177.376 4271 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 5.06 % Allowed : 20.25 % Favored : 74.68 % 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: 0.93 (0.29), residues: 760 helix: 1.34 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -1.17 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 32 TYR 0.056 0.002 TYR S 80 PHE 0.015 0.002 PHE O 67 HIS 0.004 0.001 HIS O 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.17 (13403) covalent geometry : angle 0.70239 / 0.40 (19459) hydrogen bonds : bond 0.07644 / 8.47 ( 792) hydrogen bonds : angle 3.31417 / 4.34 ( 1932) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: J 27 GLN cc_start: 0.7688 (mm-40) cc_final: 0.7383 (tm-30) REVERT: J 84 MET cc_start: 0.7980 (tpp) cc_final: 0.7713 (mmt) REVERT: J 91 LYS cc_start: 0.8941 (ttpp) cc_final: 0.8624 (ttpp) REVERT: K 25 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.7782 (t80) REVERT: M 48 ASP cc_start: 0.8295 (p0) cc_final: 0.8087 (p0) REVERT: O 54 TYR cc_start: 0.8747 (m-80) cc_final: 0.8470 (m-80) REVERT: O 97 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7798 (mt-10) REVERT: Q 77 LYS cc_start: 0.7934 (mmmt) cc_final: 0.7645 (mmmt) REVERT: Q 84 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7704 (mpp) outliers start: 32 outliers final: 23 residues processed: 149 average time/residue: 0.1561 time to fit residues: 31.0623 Evaluate side-chains 149 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 90 MET Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 84 MET Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 24 GLN Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain S residue 76 ARG Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 97 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 44 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 63 optimal weight: 0.1980 chunk 76 optimal weight: 0.5980 chunk 94 optimal weight: 8.9990 chunk 72 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 85 GLN ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** 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 = 0.4396 r_free = 0.4396 target = 0.175054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.128544 restraints weight = 20322.606| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 1.51 r_work: 0.3613 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13403 Z= 0.181 Angle : 0.700 8.181 19459 Z= 0.402 Chirality : 0.050 0.336 2218 Planarity : 0.004 0.041 1377 Dihedral : 33.939 177.239 4271 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 6.01 % Allowed : 19.30 % Favored : 74.68 % 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: 1.13 (0.30), residues: 760 helix: 1.52 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -1.20 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 20 TYR 0.055 0.002 TYR S 80 PHE 0.015 0.002 PHE O 67 HIS 0.009 0.001 HIS S 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.18 (13403) covalent geometry : angle 0.69951 / 0.40 (19459) hydrogen bonds : bond 0.07481 / 8.28 ( 792) hydrogen bonds : angle 3.27766 / 4.32 ( 1932) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 130 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: J 27 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7398 (tm-30) REVERT: J 84 MET cc_start: 0.7992 (tpp) cc_final: 0.7721 (mmt) REVERT: J 91 LYS cc_start: 0.8960 (ttpp) cc_final: 0.8638 (ttpp) REVERT: K 25 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.7683 (t80) REVERT: M 90 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: M 106 HIS cc_start: 0.8463 (OUTLIER) cc_final: 0.8199 (m170) REVERT: Q 77 LYS cc_start: 0.7939 (mmmt) cc_final: 0.7640 (mmmt) REVERT: Q 85 ASP cc_start: 0.8661 (m-30) cc_final: 0.8447 (m-30) outliers start: 38 outliers final: 27 residues processed: 153 average time/residue: 0.1597 time to fit residues: 32.4295 Evaluate side-chains 156 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 106 HIS Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 85 GLN Chi-restraints excluded: chain O residue 90 MET Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 91 LYS Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 2 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 72 optimal weight: 0.3980 chunk 7 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 0.0070 chunk 9 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** 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 = 0.4386 r_free = 0.4386 target = 0.174061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.127516 restraints weight = 20365.991| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.51 r_work: 0.3603 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13403 Z= 0.178 Angle : 0.698 8.488 19459 Z= 0.401 Chirality : 0.050 0.336 2218 Planarity : 0.004 0.039 1377 Dihedral : 33.938 176.756 4271 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.22 % Allowed : 20.73 % Favored : 74.05 % 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: 1.19 (0.30), residues: 760 helix: 1.57 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -1.19 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 32 TYR 0.053 0.002 TYR S 80 PHE 0.015 0.002 PHE O 67 HIS 0.003 0.001 HIS O 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.18 (13403) covalent geometry : angle 0.69763 / 0.40 (19459) hydrogen bonds : bond 0.07362 / 8.14 ( 792) hydrogen bonds : angle 3.23743 / 4.25 ( 1932) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: J 27 GLN cc_start: 0.7755 (mm-40) cc_final: 0.7464 (tm-30) REVERT: J 84 MET cc_start: 0.7976 (tpp) cc_final: 0.7728 (mmt) REVERT: J 91 LYS cc_start: 0.8956 (ttpp) cc_final: 0.8622 (ttpp) REVERT: K 25 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.7583 (t80) REVERT: M 37 TYR cc_start: 0.8577 (m-80) cc_final: 0.8209 (m-10) REVERT: M 90 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: M 106 HIS cc_start: 0.8437 (OUTLIER) cc_final: 0.8213 (m170) REVERT: O 97 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7870 (mt-10) REVERT: Q 77 LYS cc_start: 0.7960 (mmmt) cc_final: 0.7650 (mmmt) REVERT: Q 84 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7706 (mpp) REVERT: Q 85 ASP cc_start: 0.8563 (m-30) cc_final: 0.8331 (m-30) outliers start: 33 outliers final: 27 residues processed: 150 average time/residue: 0.1466 time to fit residues: 29.0949 Evaluate side-chains 158 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 106 HIS Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 90 MET Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 84 MET Chi-restraints excluded: chain Q residue 91 LYS Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 76 ARG Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 37 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 48 optimal weight: 0.0060 chunk 59 optimal weight: 0.7980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.173819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.127430 restraints weight = 20411.388| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.56 r_work: 0.3605 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13403 Z= 0.162 Angle : 0.684 7.534 19459 Z= 0.394 Chirality : 0.049 0.336 2218 Planarity : 0.004 0.039 1377 Dihedral : 33.888 176.794 4271 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.54 % Allowed : 20.41 % Favored : 74.05 % 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: 1.37 (0.30), residues: 760 helix: 1.72 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -1.16 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 129 TYR 0.050 0.002 TYR S 80 PHE 0.016 0.002 PHE O 67 HIS 0.008 0.001 HIS S 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.16 (13403) covalent geometry : angle 0.68411 / 0.39 (19459) hydrogen bonds : bond 0.07173 / 7.93 ( 792) hydrogen bonds : angle 3.15901 / 4.16 ( 1932) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: I 125 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8099 (mt0) REVERT: J 27 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7468 (tm-30) REVERT: J 84 MET cc_start: 0.7944 (tpp) cc_final: 0.7515 (mmt) REVERT: J 88 TYR cc_start: 0.8937 (m-10) cc_final: 0.8653 (m-10) REVERT: K 25 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.7597 (t80) REVERT: M 30 ARG cc_start: 0.7312 (ptm160) cc_final: 0.6975 (ptm160) REVERT: M 48 ASP cc_start: 0.8128 (p0) cc_final: 0.7812 (p0) REVERT: M 90 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: M 106 HIS cc_start: 0.8440 (OUTLIER) cc_final: 0.8225 (m170) REVERT: O 42 ARG cc_start: 0.7659 (mpt180) cc_final: 0.7442 (mpt180) REVERT: O 97 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7879 (mt-10) REVERT: Q 77 LYS cc_start: 0.7967 (mmmt) cc_final: 0.7661 (mmmt) REVERT: R 107 VAL cc_start: 0.8837 (p) cc_final: 0.8563 (m) outliers start: 35 outliers final: 24 residues processed: 156 average time/residue: 0.1475 time to fit residues: 30.8634 Evaluate side-chains 156 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain I residue 125 GLN Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 106 HIS Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 90 MET Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 91 LYS Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 88 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 80 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 72 optimal weight: 0.2980 chunk 41 optimal weight: 0.4980 chunk 86 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 38 ASN ** M 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 GLN ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.171966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.125701 restraints weight = 20235.546| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.53 r_work: 0.3578 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13403 Z= 0.172 Angle : 0.695 7.775 19459 Z= 0.397 Chirality : 0.050 0.327 2218 Planarity : 0.004 0.040 1377 Dihedral : 33.883 176.808 4271 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.91 % Allowed : 20.73 % Favored : 74.37 % 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: 1.39 (0.30), residues: 760 helix: 1.74 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -1.19 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 20 TYR 0.050 0.002 TYR S 80 PHE 0.013 0.002 PHE J 100 HIS 0.004 0.001 HIS S 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.17 (13403) covalent geometry : angle 0.69486 / 0.40 (19459) hydrogen bonds : bond 0.07148 / 7.90 ( 792) hydrogen bonds : angle 3.18183 / 4.16 ( 1932) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: J 27 GLN cc_start: 0.7700 (mm-40) cc_final: 0.7475 (tm-30) REVERT: J 84 MET cc_start: 0.7933 (tpp) cc_final: 0.7477 (mmt) REVERT: J 88 TYR cc_start: 0.8945 (m-10) cc_final: 0.8666 (m-10) REVERT: J 91 LYS cc_start: 0.8964 (ttpp) cc_final: 0.8650 (ttpp) REVERT: K 25 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.7493 (t80) REVERT: M 30 ARG cc_start: 0.7309 (ptm160) cc_final: 0.6889 (ptm160) REVERT: M 48 ASP cc_start: 0.8123 (p0) cc_final: 0.7809 (p0) REVERT: M 90 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: M 106 HIS cc_start: 0.8462 (OUTLIER) cc_final: 0.8249 (m170) REVERT: O 85 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.7107 (pt0) REVERT: O 97 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7906 (mt-10) REVERT: Q 77 LYS cc_start: 0.8015 (mmmt) cc_final: 0.7724 (mmmt) REVERT: R 107 VAL cc_start: 0.8819 (p) cc_final: 0.8542 (m) outliers start: 31 outliers final: 26 residues processed: 149 average time/residue: 0.1479 time to fit residues: 29.3010 Evaluate side-chains 157 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain M residue 106 HIS Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 85 GLN Chi-restraints excluded: chain O residue 90 MET Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain R residue 24 GLN Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 76 ARG Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 82 LYS Chi-restraints excluded: chain S residue 88 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 53 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 GLN R 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.168399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.121559 restraints weight = 20237.285| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.54 r_work: 0.3517 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 13403 Z= 0.229 Angle : 0.742 7.931 19459 Z= 0.418 Chirality : 0.052 0.358 2218 Planarity : 0.005 0.040 1377 Dihedral : 33.942 175.914 4271 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 5.06 % Allowed : 21.20 % Favored : 73.73 % 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: 1.06 (0.30), residues: 760 helix: 1.49 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -1.30 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 83 TYR 0.057 0.002 TYR S 80 PHE 0.033 0.003 PHE O 84 HIS 0.007 0.002 HIS S 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.23 (13403) covalent geometry : angle 0.74233 / 0.42 (19459) hydrogen bonds : bond 0.07381 / 8.16 ( 792) hydrogen bonds : angle 3.34665 / 4.36 ( 1932) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.308 Fit side-chains REVERT: J 27 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7476 (tm-30) REVERT: K 25 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.7659 (t80) REVERT: M 30 ARG cc_start: 0.7288 (ptm160) cc_final: 0.6842 (ptm160) REVERT: M 48 ASP cc_start: 0.8204 (p0) cc_final: 0.7903 (p0) REVERT: M 90 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: M 106 HIS cc_start: 0.8472 (OUTLIER) cc_final: 0.8245 (m170) REVERT: O 42 ARG cc_start: 0.7869 (mpt180) cc_final: 0.7651 (mpt180) REVERT: O 97 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7955 (mt-10) REVERT: Q 77 LYS cc_start: 0.8087 (mmmt) cc_final: 0.7795 (mmmt) REVERT: Q 84 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7849 (mpp) REVERT: R 107 VAL cc_start: 0.8875 (p) cc_final: 0.8609 (m) outliers start: 32 outliers final: 25 residues processed: 140 average time/residue: 0.1393 time to fit residues: 25.8368 Evaluate side-chains 152 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain M residue 106 HIS Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 85 GLN Chi-restraints excluded: chain O residue 90 MET Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 84 MET Chi-restraints excluded: chain R residue 24 GLN Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 82 LYS Chi-restraints excluded: chain S residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 50 optimal weight: 0.0980 chunk 7 optimal weight: 6.9990 chunk 55 optimal weight: 0.5980 chunk 100 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 32 optimal weight: 0.0970 chunk 53 optimal weight: 0.9980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.169778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.123526 restraints weight = 20148.666| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.52 r_work: 0.3556 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13403 Z= 0.160 Angle : 0.700 7.951 19459 Z= 0.399 Chirality : 0.050 0.320 2218 Planarity : 0.004 0.041 1377 Dihedral : 33.907 176.439 4271 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.75 % Allowed : 21.20 % Favored : 74.05 % 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: 1.28 (0.30), residues: 760 helix: 1.68 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -1.28 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 83 TYR 0.052 0.002 TYR S 80 PHE 0.016 0.002 PHE O 67 HIS 0.003 0.001 HIS R 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.16 (13403) covalent geometry : angle 0.70001 / 0.40 (19459) hydrogen bonds : bond 0.07111 / 7.88 ( 792) hydrogen bonds : angle 3.20831 / 4.19 ( 1932) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: J 27 GLN cc_start: 0.7711 (mm-40) cc_final: 0.7469 (tm-30) REVERT: J 84 MET cc_start: 0.7953 (tpp) cc_final: 0.7685 (mmt) REVERT: J 91 LYS cc_start: 0.8950 (ttpp) cc_final: 0.8682 (ttpp) REVERT: K 25 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.7536 (t80) REVERT: M 30 ARG cc_start: 0.7286 (ptm160) cc_final: 0.6843 (ptm160) REVERT: M 48 ASP cc_start: 0.8156 (p0) cc_final: 0.7848 (p0) REVERT: M 90 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: M 106 HIS cc_start: 0.8449 (OUTLIER) cc_final: 0.8246 (m170) REVERT: O 97 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7888 (mt-10) REVERT: Q 77 LYS cc_start: 0.7978 (mmmt) cc_final: 0.7696 (mmmt) REVERT: Q 84 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7722 (mpp) REVERT: R 107 VAL cc_start: 0.8848 (p) cc_final: 0.8572 (m) outliers start: 30 outliers final: 23 residues processed: 142 average time/residue: 0.1367 time to fit residues: 25.9813 Evaluate side-chains 156 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain M residue 106 HIS Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 85 GLN Chi-restraints excluded: chain O residue 90 MET Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 84 MET Chi-restraints excluded: chain R residue 24 GLN Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 76 optimal weight: 0.1980 chunk 16 optimal weight: 0.0570 chunk 59 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 chunk 39 optimal weight: 0.3980 chunk 48 optimal weight: 0.0470 chunk 54 optimal weight: 0.0870 chunk 46 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 overall best weight: 0.1574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 44 GLN O 85 GLN Q 93 GLN ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.172191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.126662 restraints weight = 20316.761| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.51 r_work: 0.3595 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13403 Z= 0.145 Angle : 0.672 7.085 19459 Z= 0.388 Chirality : 0.049 0.318 2218 Planarity : 0.004 0.040 1377 Dihedral : 33.808 178.535 4271 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.27 % Allowed : 21.68 % Favored : 74.05 % 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: 1.58 (0.30), residues: 760 helix: 1.92 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.27 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 42 TYR 0.045 0.002 TYR S 80 PHE 0.014 0.002 PHE O 67 HIS 0.007 0.001 HIS O 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.15 (13403) covalent geometry : angle 0.67244 / 0.39 (19459) hydrogen bonds : bond 0.06998 / 7.77 ( 792) hydrogen bonds : angle 3.06610 / 4.02 ( 1932) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2969.23 seconds wall clock time: 51 minutes 33.50 seconds (3093.50 seconds total)