Starting phenix.real_space_refine on Wed May 14 22:56:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vob_43373/05_2025/8vob_43373.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vob_43373/05_2025/8vob_43373.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/8vob_43373/05_2025/8vob_43373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vob_43373/05_2025/8vob_43373.map" model { file = "/net/cci-nas-00/data/ceres_data/8vob_43373/05_2025/8vob_43373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vob_43373/05_2025/8vob_43373.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.042 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 6897 2.51 5 N 2356 2.21 5 O 2969 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12550 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: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 835 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 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: 7.50, per 1000 atoms: 0.60 Number of scatterers: 12550 At special positions: 0 Unit cell: (112.35, 136.5, 119.7, 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 2969 8.00 N 2356 7.00 C 6897 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: 2.86 Conformation dependent library (CDL) restraints added in 882.3 milliseconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1454 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 71.2% alpha, 2.3% beta 155 base pairs and 266 stacking pairs defined. Time for finding SS restraints: 5.86 Creating SS restraints... Processing helix chain 'I' and resid 45 through 56 removed outlier: 3.504A pdb=" N LYS I 56 " --> pdb=" O ARG I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 76 Processing helix chain 'I' and resid 85 through 114 Processing helix chain 'I' and resid 120 through 131 Processing helix chain 'J' and resid 24 through 29 Processing helix chain 'J' and resid 30 through 42 Processing helix chain 'J' and resid 50 through 76 removed outlier: 3.840A pdb=" N ASP J 68 " --> pdb=" O ASN J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 94 removed outlier: 3.664A pdb=" N VAL J 86 " --> pdb=" O THR J 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 21 Processing helix chain 'K' and resid 26 through 37 Processing helix chain 'K' and resid 45 through 73 removed outlier: 4.320A pdb=" N VAL K 49 " --> pdb=" O ALA K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 88 Processing helix chain 'K' and resid 90 through 98 removed outlier: 3.994A pdb=" N LEU K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 116 Processing helix chain 'M' and resid 34 through 46 Processing helix chain 'M' and resid 52 through 81 Processing helix chain 'M' and resid 87 through 99 removed outlier: 3.809A pdb=" N ILE M 91 " --> pdb=" O THR M 87 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU M 99 " --> pdb=" O VAL M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 101 through 121 removed outlier: 3.726A pdb=" N ALA M 121 " --> pdb=" O LYS M 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 55 Processing helix chain 'O' and resid 63 through 79 removed outlier: 3.983A pdb=" N PHE O 67 " --> pdb=" O ARG O 63 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE O 78 " --> pdb=" O ILE O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 132 removed outlier: 3.714A pdb=" N ILE O 124 " --> pdb=" O MET O 120 " (cutoff:3.500A) 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 76 removed outlier: 4.387A pdb=" N GLU Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG Q 55 " --> pdb=" O TYR Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 93 removed outlier: 3.609A pdb=" N VAL Q 86 " --> pdb=" O THR Q 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 21 removed outlier: 3.649A pdb=" N ARG R 20 " --> pdb=" O THR R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 37 Processing helix chain 'R' and resid 45 through 73 removed outlier: 4.296A pdb=" N VAL R 49 " --> pdb=" O ALA R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 90 Processing helix chain 'R' and resid 90 through 97 Processing helix chain 'R' and resid 112 through 116 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 removed outlier: 3.514A pdb=" N ILE S 91 " --> pdb=" O THR S 87 " (cutoff:3.500A) Processing helix chain 'S' and resid 101 through 121 removed outlier: 4.038A pdb=" N LYS S 105 " --> pdb=" O GLY S 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 83 through 84 removed outlier: 7.590A 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 removed outlier: 3.515A pdb=" N ILE I 119 " --> pdb=" O ARG J 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'J' and resid 96 through 97 removed outlier: 6.336A 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: 7.566A 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 77 through 78 Processing sheet with id=AA6, first strand: chain 'K' and resid 101 through 102 removed outlier: 7.048A pdb=" N THR K 101 " --> pdb=" O TYR Q 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.767A pdb=" N ARG O 83 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'R' and resid 42 through 43 removed outlier: 7.333A pdb=" N ARG R 42 " --> pdb=" O ILE S 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'R' and resid 77 through 78 396 hydrogen bonds defined for protein. 1161 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 395 hydrogen bonds 758 hydrogen bond angles 0 basepair planarities 155 basepair parallelities 266 stacking parallelities Total time for adding SS restraints: 5.10 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2633 1.33 - 1.46: 4388 1.46 - 1.58: 5741 1.58 - 1.70: 627 1.70 - 1.82: 24 Bond restraints: 13413 Sorted by residual: bond pdb=" CG PRO Q 32 " pdb=" CD PRO Q 32 " ideal model delta sigma weight residual 1.503 1.300 0.203 3.40e-02 8.65e+02 3.55e+01 bond pdb=" N PRO Q 32 " pdb=" CD PRO Q 32 " ideal model delta sigma weight residual 1.473 1.525 -0.052 1.40e-02 5.10e+03 1.40e+01 bond pdb=" CB PRO Q 32 " pdb=" CG PRO Q 32 " ideal model delta sigma weight residual 1.492 1.663 -0.171 5.00e-02 4.00e+02 1.16e+01 bond pdb=" N PRO Q 32 " pdb=" CA PRO Q 32 " ideal model delta sigma weight residual 1.472 1.438 0.034 1.34e-02 5.57e+03 6.45e+00 bond pdb=" C3' DA H 20 " pdb=" O3' DA H 20 " ideal model delta sigma weight residual 1.422 1.477 -0.055 3.00e-02 1.11e+03 3.33e+00 ... (remaining 13408 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.74: 19394 3.74 - 7.48: 71 7.48 - 11.21: 8 11.21 - 14.95: 1 14.95 - 18.69: 1 Bond angle restraints: 19475 Sorted by residual: angle pdb=" CA PRO Q 32 " pdb=" N PRO Q 32 " pdb=" CD PRO Q 32 " ideal model delta sigma weight residual 112.00 93.31 18.69 1.40e+00 5.10e-01 1.78e+02 angle pdb=" N PRO Q 32 " pdb=" CD PRO Q 32 " pdb=" CG PRO Q 32 " ideal model delta sigma weight residual 103.20 90.45 12.75 1.50e+00 4.44e-01 7.23e+01 angle pdb=" N VAL I 117 " pdb=" CA VAL I 117 " pdb=" C VAL I 117 " ideal model delta sigma weight residual 113.71 109.03 4.68 9.50e-01 1.11e+00 2.42e+01 angle pdb=" CA PRO Q 32 " pdb=" CB PRO Q 32 " pdb=" CG PRO Q 32 " ideal model delta sigma weight residual 104.50 95.21 9.29 1.90e+00 2.77e-01 2.39e+01 angle pdb=" CA ASN K 73 " pdb=" CB ASN K 73 " pdb=" CG ASN K 73 " ideal model delta sigma weight residual 112.60 117.30 -4.70 1.00e+00 1.00e+00 2.21e+01 ... (remaining 19470 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 5759 35.96 - 71.93: 1405 71.93 - 107.89: 30 107.89 - 143.86: 8 143.86 - 179.82: 24 Dihedral angle restraints: 7226 sinusoidal: 4973 harmonic: 2253 Sorted by residual: dihedral pdb=" C4' DT D 225 " pdb=" C3' DT D 225 " pdb=" O3' DT D 225 " pdb=" P DT D 226 " ideal model delta sinusoidal sigma weight residual 220.00 40.18 179.82 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC D 162 " pdb=" C3' DC D 162 " pdb=" O3' DC D 162 " pdb=" P DC D 163 " ideal model delta sinusoidal sigma weight residual -140.00 39.60 -179.60 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG D 231 " pdb=" C3' DG D 231 " pdb=" O3' DG D 231 " pdb=" P DC D 232 " ideal model delta sinusoidal sigma weight residual 220.00 40.77 179.23 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 7223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2058 0.070 - 0.140: 153 0.140 - 0.209: 7 0.209 - 0.279: 1 0.279 - 0.349: 1 Chirality restraints: 2220 Sorted by residual: chirality pdb=" CG LEU Q 62 " pdb=" CB LEU Q 62 " pdb=" CD1 LEU Q 62 " pdb=" CD2 LEU Q 62 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CB ILE O 62 " pdb=" CA ILE O 62 " pdb=" CG1 ILE O 62 " pdb=" CG2 ILE O 62 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA LEU Q 62 " pdb=" N LEU Q 62 " pdb=" C LEU Q 62 " pdb=" CB LEU Q 62 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.56e-01 ... (remaining 2217 not shown) Planarity restraints: 1378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS Q 31 " -0.108 5.00e-02 4.00e+02 1.47e-01 3.43e+01 pdb=" N PRO Q 32 " 0.252 5.00e-02 4.00e+02 pdb=" CA PRO Q 32 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO Q 32 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU Q 63 " 0.013 2.00e-02 2.50e+03 2.75e-02 7.58e+00 pdb=" CD GLU Q 63 " -0.048 2.00e-02 2.50e+03 pdb=" OE1 GLU Q 63 " 0.017 2.00e-02 2.50e+03 pdb=" OE2 GLU Q 63 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC H 114 " 0.002 2.00e-02 2.50e+03 1.65e-02 6.12e+00 pdb=" N1 DC H 114 " -0.011 2.00e-02 2.50e+03 pdb=" C2 DC H 114 " 0.041 2.00e-02 2.50e+03 pdb=" O2 DC H 114 " -0.022 2.00e-02 2.50e+03 pdb=" N3 DC H 114 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DC H 114 " 0.007 2.00e-02 2.50e+03 pdb=" N4 DC H 114 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DC H 114 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DC H 114 " -0.003 2.00e-02 2.50e+03 ... (remaining 1375 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 269 2.63 - 3.20: 10907 3.20 - 3.77: 25129 3.77 - 4.33: 30746 4.33 - 4.90: 43494 Nonbonded interactions: 110545 Sorted by model distance: nonbonded pdb=" N2 DG H 137 " pdb=" O2 DC D 178 " model vdw 2.066 2.496 nonbonded pdb=" O2 DC H 110 " pdb=" N2 DG D 205 " model vdw 2.123 2.496 nonbonded pdb=" N2 DG H 135 " pdb=" O2 DC D 180 " model vdw 2.137 2.496 nonbonded pdb=" O2 DC H 154 " pdb=" N2 DG D 161 " model vdw 2.144 2.496 nonbonded pdb=" N2 DG H 93 " pdb=" O2 DC D 222 " model vdw 2.153 2.496 ... (remaining 110540 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: 3.580 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: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.340 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 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 : 0.005 0.203 13413 Z= 0.201 Angle : 0.759 18.688 19475 Z= 0.445 Chirality : 0.039 0.349 2220 Planarity : 0.006 0.147 1378 Dihedral : 31.207 179.822 5772 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.79 % Allowed : 31.80 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.31), residues: 759 helix: 1.49 (0.23), residues: 519 sheet: None (None), residues: 0 loop : -1.50 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 75 PHE 0.012 0.002 PHE M 67 TYR 0.023 0.002 TYR K 57 ARG 0.008 0.001 ARG S 76 Details of bonding type rmsd hydrogen bonds : bond 0.10427 ( 791) hydrogen bonds : angle 3.77246 ( 1919) covalent geometry : bond 0.00481 (13413) covalent geometry : angle 0.75903 (19475) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 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: 5 poor density : 160 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 161 average time/residue: 0.2808 time to fit residues: 62.0115 Evaluate side-chains 155 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 105 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 20.0000 chunk 41 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 68 GLN ** 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 = 0.3998 r_free = 0.3998 target = 0.067297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.054591 restraints weight = 67230.813| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.94 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13413 Z= 0.182 Angle : 0.652 7.445 19475 Z= 0.378 Chirality : 0.037 0.209 2220 Planarity : 0.005 0.064 1378 Dihedral : 33.823 178.729 4280 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.53 % Allowed : 26.27 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.31), residues: 759 helix: 1.62 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -1.26 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS J 75 PHE 0.014 0.001 PHE M 62 TYR 0.032 0.002 TYR S 80 ARG 0.003 0.000 ARG Q 92 Details of bonding type rmsd hydrogen bonds : bond 0.06484 ( 791) hydrogen bonds : angle 3.22955 ( 1919) covalent geometry : bond 0.00414 (13413) covalent geometry : angle 0.65172 (19475) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 37 LYS cc_start: 0.8757 (tppt) cc_final: 0.8554 (tptp) REVERT: I 50 GLU cc_start: 0.9325 (pt0) cc_final: 0.9059 (pt0) REVERT: I 64 LYS cc_start: 0.8627 (mmmt) cc_final: 0.8222 (mmmt) REVERT: J 78 ARG cc_start: 0.8172 (ptp90) cc_final: 0.7959 (ptp90) REVERT: K 64 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7999 (mm-30) REVERT: M 54 LYS cc_start: 0.8776 (pttm) cc_final: 0.8409 (ptmt) REVERT: M 92 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8314 (tm-30) REVERT: O 90 MET cc_start: 0.8437 (mpp) cc_final: 0.8057 (mmm) REVERT: Q 93 GLN cc_start: 0.8679 (mm110) cc_final: 0.8369 (mm110) REVERT: R 84 GLN cc_start: 0.8869 (tp40) cc_final: 0.8553 (tp40) REVERT: R 118 LYS cc_start: 0.5625 (mmmm) cc_final: 0.5383 (mtpp) REVERT: S 44 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8682 (mm110) REVERT: S 68 GLU cc_start: 0.8682 (pp20) cc_final: 0.8462 (tp30) outliers start: 16 outliers final: 5 residues processed: 174 average time/residue: 0.2688 time to fit residues: 65.0813 Evaluate side-chains 152 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 146 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 92 GLN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain R residue 114 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 45 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 60 ASN ** M 81 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 = 0.3914 r_free = 0.3914 target = 0.063835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.051025 restraints weight = 69030.340| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 3.02 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 13413 Z= 0.251 Angle : 0.685 5.150 19475 Z= 0.399 Chirality : 0.039 0.158 2220 Planarity : 0.005 0.062 1378 Dihedral : 34.077 179.697 4276 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.16 % Allowed : 26.42 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.30), residues: 759 helix: 1.46 (0.23), residues: 517 sheet: None (None), residues: 0 loop : -1.39 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS J 75 PHE 0.012 0.002 PHE M 62 TYR 0.047 0.003 TYR Q 88 ARG 0.006 0.001 ARG Q 92 Details of bonding type rmsd hydrogen bonds : bond 0.07080 ( 791) hydrogen bonds : angle 3.32644 ( 1919) covalent geometry : bond 0.00567 (13413) covalent geometry : angle 0.68538 (19475) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 50 GLU cc_start: 0.9376 (pt0) cc_final: 0.9052 (pt0) REVERT: I 60 LEU cc_start: 0.8743 (mm) cc_final: 0.8497 (mm) REVERT: I 93 GLN cc_start: 0.8775 (tt0) cc_final: 0.8539 (tt0) REVERT: K 64 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7911 (mm-30) REVERT: K 65 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8310 (mm) REVERT: M 54 LYS cc_start: 0.8727 (pttm) cc_final: 0.8467 (ptpt) REVERT: M 92 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8268 (tm-30) REVERT: O 120 MET cc_start: 0.7482 (mmt) cc_final: 0.7277 (mmt) REVERT: R 84 GLN cc_start: 0.8875 (tp40) cc_final: 0.8493 (tp40) REVERT: S 68 GLU cc_start: 0.8767 (pp20) cc_final: 0.8431 (tp30) REVERT: S 103 LEU cc_start: 0.9428 (mt) cc_final: 0.9217 (mt) outliers start: 20 outliers final: 12 residues processed: 178 average time/residue: 0.3034 time to fit residues: 72.9967 Evaluate side-chains 158 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 92 GLN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 74 ILE Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain S residue 29 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 31 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.065891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.053033 restraints weight = 67031.639| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.95 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13413 Z= 0.178 Angle : 0.651 8.931 19475 Z= 0.378 Chirality : 0.037 0.148 2220 Planarity : 0.004 0.061 1378 Dihedral : 33.950 179.180 4276 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.06 % Allowed : 28.96 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.30), residues: 759 helix: 1.63 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -1.46 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS M 79 PHE 0.009 0.001 PHE I 67 TYR 0.035 0.002 TYR Q 88 ARG 0.005 0.000 ARG Q 95 Details of bonding type rmsd hydrogen bonds : bond 0.06336 ( 791) hydrogen bonds : angle 3.19384 ( 1919) covalent geometry : bond 0.00403 (13413) covalent geometry : angle 0.65124 (19475) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 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: 13 poor density : 175 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 50 GLU cc_start: 0.9326 (pt0) cc_final: 0.9085 (pt0) REVERT: I 60 LEU cc_start: 0.8518 (mm) cc_final: 0.8125 (mm) REVERT: I 64 LYS cc_start: 0.8540 (mmmt) cc_final: 0.8328 (mmmt) REVERT: I 93 GLN cc_start: 0.8723 (tt0) cc_final: 0.8391 (tt0) REVERT: K 61 GLU cc_start: 0.8501 (tp30) cc_final: 0.7320 (tp30) REVERT: K 65 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8269 (mm) REVERT: K 92 GLU cc_start: 0.9077 (pm20) cc_final: 0.8852 (pm20) REVERT: M 39 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.7942 (t80) REVERT: M 42 LEU cc_start: 0.9235 (pp) cc_final: 0.8900 (tp) REVERT: M 54 LYS cc_start: 0.8668 (pttm) cc_final: 0.8360 (ptmt) REVERT: M 92 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8293 (tm-30) REVERT: O 90 MET cc_start: 0.8687 (mmm) cc_final: 0.8288 (mmm) REVERT: Q 59 LYS cc_start: 0.8141 (mttt) cc_final: 0.7766 (mtmm) REVERT: R 84 GLN cc_start: 0.8828 (tp40) cc_final: 0.8408 (tp40) REVERT: S 42 LEU cc_start: 0.8655 (mt) cc_final: 0.8306 (tp) REVERT: S 68 GLU cc_start: 0.8760 (pp20) cc_final: 0.8459 (tp30) REVERT: S 73 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8429 (mm-30) REVERT: S 103 LEU cc_start: 0.9409 (mt) cc_final: 0.9198 (mt) outliers start: 13 outliers final: 4 residues processed: 183 average time/residue: 0.2772 time to fit residues: 69.3024 Evaluate side-chains 161 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 154 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 39 TYR Chi-restraints excluded: chain M residue 92 GLN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain Q residue 71 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 16 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.064705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.051938 restraints weight = 68653.605| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.94 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13413 Z= 0.209 Angle : 0.660 7.118 19475 Z= 0.385 Chirality : 0.038 0.161 2220 Planarity : 0.005 0.062 1378 Dihedral : 34.009 179.591 4276 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.85 % Allowed : 29.11 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.31), residues: 759 helix: 1.61 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -1.64 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 113 PHE 0.011 0.001 PHE I 67 TYR 0.051 0.002 TYR S 80 ARG 0.007 0.000 ARG Q 92 Details of bonding type rmsd hydrogen bonds : bond 0.06571 ( 791) hydrogen bonds : angle 3.26644 ( 1919) covalent geometry : bond 0.00472 (13413) covalent geometry : angle 0.65992 (19475) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 60 LEU cc_start: 0.8631 (mm) cc_final: 0.8319 (mm) REVERT: I 64 LYS cc_start: 0.8437 (mmmt) cc_final: 0.8154 (mmmt) REVERT: I 93 GLN cc_start: 0.8747 (tt0) cc_final: 0.8279 (tt0) REVERT: K 65 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8218 (mm) REVERT: M 54 LYS cc_start: 0.8706 (pttm) cc_final: 0.8445 (ptmt) REVERT: M 92 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8298 (tm-30) REVERT: O 90 MET cc_start: 0.8707 (mmm) cc_final: 0.8316 (mmm) REVERT: O 93 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.6873 (tt0) REVERT: R 84 GLN cc_start: 0.8845 (tp40) cc_final: 0.8394 (tp40) REVERT: S 68 GLU cc_start: 0.8747 (pp20) cc_final: 0.8455 (tp30) outliers start: 18 outliers final: 8 residues processed: 176 average time/residue: 0.2769 time to fit residues: 66.9762 Evaluate side-chains 164 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain M residue 92 GLN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 74 ILE Chi-restraints excluded: chain O residue 93 GLN Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain R residue 114 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 101 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 43 optimal weight: 0.0050 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 73 ASN Q 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.064544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.051825 restraints weight = 68563.959| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.95 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13413 Z= 0.202 Angle : 0.673 9.769 19475 Z= 0.390 Chirality : 0.037 0.162 2220 Planarity : 0.005 0.061 1378 Dihedral : 33.998 179.719 4276 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.69 % Allowed : 29.43 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.30), residues: 759 helix: 1.57 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -1.57 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 113 PHE 0.012 0.001 PHE I 67 TYR 0.064 0.002 TYR S 80 ARG 0.005 0.000 ARG S 76 Details of bonding type rmsd hydrogen bonds : bond 0.06498 ( 791) hydrogen bonds : angle 3.28652 ( 1919) covalent geometry : bond 0.00458 (13413) covalent geometry : angle 0.67303 (19475) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 60 LEU cc_start: 0.8553 (mm) cc_final: 0.8010 (mm) REVERT: I 93 GLN cc_start: 0.8752 (tt0) cc_final: 0.8321 (tt0) REVERT: I 125 GLN cc_start: 0.9362 (mt0) cc_final: 0.9156 (mt0) REVERT: K 65 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8246 (mm) REVERT: M 42 LEU cc_start: 0.9266 (pp) cc_final: 0.8841 (tp) REVERT: M 54 LYS cc_start: 0.8699 (pttm) cc_final: 0.8458 (ptmt) REVERT: M 92 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8320 (tm-30) REVERT: O 93 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.6816 (tt0) REVERT: Q 59 LYS cc_start: 0.8339 (mttt) cc_final: 0.7877 (mtmm) REVERT: R 84 GLN cc_start: 0.8858 (tp40) cc_final: 0.8402 (tp40) REVERT: S 68 GLU cc_start: 0.8768 (pp20) cc_final: 0.8454 (tp30) REVERT: S 76 ARG cc_start: 0.8625 (ttm110) cc_final: 0.8242 (ttm170) outliers start: 17 outliers final: 10 residues processed: 178 average time/residue: 0.2981 time to fit residues: 73.5547 Evaluate side-chains 165 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 73 ASN Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 92 GLN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 74 ILE Chi-restraints excluded: chain O residue 93 GLN Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain R residue 114 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 85 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 93 GLN K 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.062399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.049796 restraints weight = 69447.749| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.99 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13413 Z= 0.258 Angle : 0.713 7.887 19475 Z= 0.413 Chirality : 0.040 0.261 2220 Planarity : 0.005 0.062 1378 Dihedral : 34.125 179.972 4276 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.48 % Allowed : 30.22 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.30), residues: 759 helix: 1.36 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -1.48 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 113 PHE 0.015 0.002 PHE I 67 TYR 0.061 0.003 TYR S 80 ARG 0.005 0.001 ARG Q 92 Details of bonding type rmsd hydrogen bonds : bond 0.07223 ( 791) hydrogen bonds : angle 3.47883 ( 1919) covalent geometry : bond 0.00581 (13413) covalent geometry : angle 0.71255 (19475) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 59 GLU cc_start: 0.7900 (pm20) cc_final: 0.7511 (pp20) REVERT: I 74 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8715 (tt) REVERT: K 65 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8291 (mm) REVERT: M 42 LEU cc_start: 0.9289 (pp) cc_final: 0.8959 (tp) REVERT: M 54 LYS cc_start: 0.8758 (pttm) cc_final: 0.8534 (ptmt) REVERT: M 92 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8358 (tm-30) REVERT: O 90 MET cc_start: 0.8744 (mmm) cc_final: 0.8218 (mmm) REVERT: O 93 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.6908 (tt0) REVERT: Q 59 LYS cc_start: 0.8342 (mttt) cc_final: 0.7927 (mtmm) REVERT: R 84 GLN cc_start: 0.8887 (tp40) cc_final: 0.8429 (tp40) REVERT: S 68 GLU cc_start: 0.8771 (pp20) cc_final: 0.8442 (tp30) REVERT: S 105 LYS cc_start: 0.9571 (OUTLIER) cc_final: 0.9352 (mtmm) outliers start: 22 outliers final: 14 residues processed: 166 average time/residue: 0.2752 time to fit residues: 62.4331 Evaluate side-chains 168 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 59 MET Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 92 GLN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 74 ILE Chi-restraints excluded: chain O residue 93 GLN Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 105 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.065094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.052435 restraints weight = 68220.489| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.97 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13413 Z= 0.184 Angle : 0.682 7.880 19475 Z= 0.394 Chirality : 0.038 0.199 2220 Planarity : 0.005 0.061 1378 Dihedral : 33.947 179.991 4276 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.74 % Allowed : 32.91 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.30), residues: 759 helix: 1.38 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -1.47 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 75 PHE 0.009 0.001 PHE I 67 TYR 0.055 0.002 TYR M 80 ARG 0.005 0.000 ARG S 76 Details of bonding type rmsd hydrogen bonds : bond 0.06404 ( 791) hydrogen bonds : angle 3.34824 ( 1919) covalent geometry : bond 0.00415 (13413) covalent geometry : angle 0.68237 (19475) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 50 GLU cc_start: 0.9329 (pt0) cc_final: 0.8941 (pt0) REVERT: J 53 GLU cc_start: 0.8776 (pt0) cc_final: 0.8532 (pt0) REVERT: K 65 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8230 (mm) REVERT: K 73 ASN cc_start: 0.9113 (t160) cc_final: 0.8861 (t0) REVERT: M 54 LYS cc_start: 0.8596 (pttm) cc_final: 0.8310 (ptmt) REVERT: M 92 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8320 (tm-30) REVERT: O 79 LYS cc_start: 0.8717 (tptp) cc_final: 0.8501 (tptp) REVERT: O 90 MET cc_start: 0.8727 (mmm) cc_final: 0.8284 (mmm) REVERT: Q 59 LYS cc_start: 0.8263 (mttt) cc_final: 0.7885 (mtmm) REVERT: Q 82 THR cc_start: 0.7520 (p) cc_final: 0.7308 (p) REVERT: R 84 GLN cc_start: 0.8835 (tp40) cc_final: 0.8356 (tp40) REVERT: S 68 GLU cc_start: 0.8776 (pp20) cc_final: 0.8448 (tp30) REVERT: S 76 ARG cc_start: 0.8392 (ttm110) cc_final: 0.8149 (ttm170) REVERT: S 97 LEU cc_start: 0.9052 (tp) cc_final: 0.8836 (tp) REVERT: S 102 GLU cc_start: 0.8902 (pt0) cc_final: 0.8600 (pp20) REVERT: S 105 LYS cc_start: 0.9569 (OUTLIER) cc_final: 0.9326 (mtmm) outliers start: 11 outliers final: 7 residues processed: 179 average time/residue: 0.2716 time to fit residues: 67.2674 Evaluate side-chains 172 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain M residue 59 MET Chi-restraints excluded: chain M residue 92 GLN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain S residue 105 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 26 optimal weight: 0.0870 chunk 59 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 overall best weight: 1.0162 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.064896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.052302 restraints weight = 68436.754| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 3.02 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13413 Z= 0.193 Angle : 0.694 10.680 19475 Z= 0.400 Chirality : 0.039 0.204 2220 Planarity : 0.005 0.056 1378 Dihedral : 33.911 179.767 4276 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.69 % Allowed : 33.70 % Favored : 63.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.30), residues: 759 helix: 1.30 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -1.52 (0.36), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS R 82 PHE 0.015 0.001 PHE M 62 TYR 0.047 0.003 TYR M 80 ARG 0.005 0.000 ARG Q 95 Details of bonding type rmsd hydrogen bonds : bond 0.06442 ( 791) hydrogen bonds : angle 3.45092 ( 1919) covalent geometry : bond 0.00439 (13413) covalent geometry : angle 0.69436 (19475) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 53 GLU cc_start: 0.8853 (pt0) cc_final: 0.8607 (pt0) REVERT: K 65 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8198 (mm) REVERT: K 73 ASN cc_start: 0.9107 (t160) cc_final: 0.8787 (t0) REVERT: M 54 LYS cc_start: 0.8648 (pttm) cc_final: 0.8377 (ptmt) REVERT: M 92 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8319 (tm-30) REVERT: O 79 LYS cc_start: 0.8726 (tptp) cc_final: 0.8499 (tptp) REVERT: O 90 MET cc_start: 0.8736 (mmm) cc_final: 0.8282 (mmm) REVERT: Q 59 LYS cc_start: 0.8243 (mttt) cc_final: 0.7856 (mtmm) REVERT: R 84 GLN cc_start: 0.8833 (tp40) cc_final: 0.8346 (tp40) REVERT: S 68 GLU cc_start: 0.8798 (pp20) cc_final: 0.8454 (tp30) REVERT: S 102 GLU cc_start: 0.8903 (pt0) cc_final: 0.8599 (pp20) REVERT: S 105 LYS cc_start: 0.9567 (OUTLIER) cc_final: 0.9321 (mtmm) outliers start: 17 outliers final: 12 residues processed: 172 average time/residue: 0.2726 time to fit residues: 64.8567 Evaluate side-chains 170 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 59 MET Chi-restraints excluded: chain M residue 92 GLN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 88 TYR Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain S residue 31 LYS Chi-restraints excluded: chain S residue 105 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 52 optimal weight: 0.0370 chunk 46 optimal weight: 0.9980 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 84 GLN ** 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 = 0.3965 r_free = 0.3965 target = 0.065927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.053353 restraints weight = 67951.491| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.97 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13413 Z= 0.185 Angle : 0.710 9.629 19475 Z= 0.405 Chirality : 0.038 0.215 2220 Planarity : 0.005 0.044 1378 Dihedral : 33.831 179.639 4276 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.53 % Allowed : 34.18 % Favored : 63.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.30), residues: 759 helix: 1.24 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.50 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS R 82 PHE 0.011 0.001 PHE O 67 TYR 0.078 0.003 TYR S 80 ARG 0.012 0.000 ARG Q 92 Details of bonding type rmsd hydrogen bonds : bond 0.06371 ( 791) hydrogen bonds : angle 3.47883 ( 1919) covalent geometry : bond 0.00422 (13413) covalent geometry : angle 0.71023 (19475) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 53 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8547 (pt0) REVERT: K 65 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8219 (mm) REVERT: K 73 ASN cc_start: 0.9120 (t160) cc_final: 0.8815 (t0) REVERT: M 54 LYS cc_start: 0.8617 (pttm) cc_final: 0.8343 (ptmt) REVERT: M 92 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8462 (tm-30) REVERT: O 79 LYS cc_start: 0.8722 (tptp) cc_final: 0.8487 (tptp) REVERT: O 90 MET cc_start: 0.8741 (mmm) cc_final: 0.8327 (mmm) REVERT: Q 59 LYS cc_start: 0.8214 (mttt) cc_final: 0.7832 (mtmm) REVERT: R 84 GLN cc_start: 0.8811 (tp40) cc_final: 0.8078 (tm-30) REVERT: S 68 GLU cc_start: 0.8765 (pp20) cc_final: 0.8422 (tp30) REVERT: S 105 LYS cc_start: 0.9559 (OUTLIER) cc_final: 0.9313 (mtmm) outliers start: 16 outliers final: 10 residues processed: 168 average time/residue: 0.2666 time to fit residues: 61.5806 Evaluate side-chains 168 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 92 GLN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 88 TYR Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain S residue 31 LYS Chi-restraints excluded: chain S residue 105 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 91 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 50 optimal weight: 0.0770 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 75 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 = 0.3881 r_free = 0.3881 target = 0.062350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.049878 restraints weight = 70738.893| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.03 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13413 Z= 0.266 Angle : 0.757 10.556 19475 Z= 0.434 Chirality : 0.042 0.233 2220 Planarity : 0.006 0.045 1378 Dihedral : 34.041 179.888 4276 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.85 % Allowed : 33.86 % Favored : 63.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.30), residues: 759 helix: 1.04 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -1.49 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS J 75 PHE 0.027 0.002 PHE M 62 TYR 0.091 0.004 TYR S 80 ARG 0.016 0.001 ARG Q 92 Details of bonding type rmsd hydrogen bonds : bond 0.07381 ( 791) hydrogen bonds : angle 3.66489 ( 1919) covalent geometry : bond 0.00602 (13413) covalent geometry : angle 0.75723 (19475) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6253.67 seconds wall clock time: 108 minutes 57.43 seconds (6537.43 seconds total)