Starting phenix.real_space_refine on Wed Sep 17 23:56:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vob_43373/09_2025/8vob_43373.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vob_43373/09_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_43373/09_2025/8vob_43373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vob_43373/09_2025/8vob_43373.map" model { file = "/net/cci-nas-00/data/ceres_data/8vob_43373/09_2025/8vob_43373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vob_43373/09_2025/8vob_43373.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= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.89, per 1000 atoms: 0.23 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: 1.07 Conformation dependent library (CDL) restraints added in 330.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.22 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: 2.74 Time building geometry restraints manager: 1.45 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: 3.830 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.480 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.110 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG S 76 TYR 0.023 0.002 TYR K 57 PHE 0.012 0.002 PHE M 67 HIS 0.003 0.001 HIS J 75 Details of bonding type rmsd covalent geometry : bond 0.00481 (13413) covalent geometry : angle 0.75903 (19475) hydrogen bonds : bond 0.10427 ( 791) hydrogen bonds : angle 3.77246 ( 1919) *********************** 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 : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 161 average time/residue: 0.1343 time to fit residues: 29.8517 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 : 0.346 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 20.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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** ** 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 = 0.3989 r_free = 0.3989 target = 0.066992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.054151 restraints weight = 67565.773| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.94 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13413 Z= 0.189 Angle : 0.655 7.071 19475 Z= 0.380 Chirality : 0.037 0.198 2220 Planarity : 0.005 0.068 1378 Dihedral : 33.836 178.993 4280 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.85 % Allowed : 25.47 % Favored : 71.68 % 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 aren not related in a simple way. whole: 1.07 (0.31), residues: 759 helix: 1.61 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -1.26 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 92 TYR 0.034 0.002 TYR Q 88 PHE 0.015 0.001 PHE M 62 HIS 0.006 0.001 HIS J 75 Details of bonding type rmsd covalent geometry : bond 0.00428 (13413) covalent geometry : angle 0.65507 (19475) hydrogen bonds : bond 0.06533 ( 791) hydrogen bonds : angle 3.23321 ( 1919) *********************** 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 186 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 37 LYS cc_start: 0.8812 (tppt) cc_final: 0.8611 (tptp) REVERT: I 50 GLU cc_start: 0.9314 (pt0) cc_final: 0.9084 (pt0) REVERT: I 64 LYS cc_start: 0.8641 (mmmt) cc_final: 0.8280 (mmmt) REVERT: J 78 ARG cc_start: 0.8119 (ptp90) cc_final: 0.7912 (ptp90) REVERT: K 64 GLU cc_start: 0.8253 (mm-30) cc_final: 0.8002 (mm-30) REVERT: M 54 LYS cc_start: 0.8777 (pttm) cc_final: 0.8419 (ptmt) REVERT: M 92 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8328 (tm-30) REVERT: O 90 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7749 (mmp) REVERT: Q 93 GLN cc_start: 0.8696 (mm110) cc_final: 0.8416 (mm110) REVERT: R 84 GLN cc_start: 0.8855 (tp40) cc_final: 0.8533 (tp40) REVERT: R 118 LYS cc_start: 0.5627 (mmmm) cc_final: 0.5387 (mtpp) REVERT: S 44 GLN cc_start: 0.8948 (mm-40) cc_final: 0.8673 (mm110) REVERT: S 68 GLU cc_start: 0.8706 (pp20) cc_final: 0.8457 (tp30) outliers start: 18 outliers final: 6 residues processed: 176 average time/residue: 0.1343 time to fit residues: 32.8906 Evaluate side-chains 153 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 82 LEU Chi-restraints excluded: chain O residue 90 MET 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 49 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 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 = 0.3885 r_free = 0.3885 target = 0.062662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.049870 restraints weight = 69663.675| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 3.05 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13413 Z= 0.282 Angle : 0.710 6.757 19475 Z= 0.414 Chirality : 0.041 0.165 2220 Planarity : 0.006 0.064 1378 Dihedral : 34.189 179.451 4276 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.32 % Allowed : 26.74 % Favored : 69.94 % 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 aren not related in a simple way. whole: 0.77 (0.30), residues: 759 helix: 1.38 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -1.38 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 92 TYR 0.051 0.003 TYR Q 88 PHE 0.013 0.002 PHE I 67 HIS 0.008 0.001 HIS J 75 Details of bonding type rmsd covalent geometry : bond 0.00630 (13413) covalent geometry : angle 0.71044 (19475) hydrogen bonds : bond 0.07558 ( 791) hydrogen bonds : angle 3.43604 ( 1919) *********************** 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 186 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 50 GLU cc_start: 0.9392 (pt0) cc_final: 0.9153 (pt0) REVERT: I 60 LEU cc_start: 0.8812 (mm) cc_final: 0.8335 (mm) REVERT: I 93 GLN cc_start: 0.8902 (tt0) cc_final: 0.8590 (tt0) REVERT: K 64 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7956 (mm-30) REVERT: K 65 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8363 (mm) REVERT: M 54 LYS cc_start: 0.8806 (pttm) cc_final: 0.8574 (ptpt) REVERT: M 92 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8331 (tm-30) REVERT: O 90 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8301 (mmt) REVERT: O 120 MET cc_start: 0.7468 (mmt) cc_final: 0.7214 (mmt) REVERT: Q 24 ASP cc_start: 0.7635 (t0) cc_final: 0.7190 (p0) REVERT: R 57 TYR cc_start: 0.8327 (t80) cc_final: 0.8024 (t80) REVERT: R 84 GLN cc_start: 0.8892 (tp40) cc_final: 0.8512 (tp40) REVERT: S 44 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8687 (mm110) REVERT: S 68 GLU cc_start: 0.8814 (pp20) cc_final: 0.8475 (tp30) REVERT: S 103 LEU cc_start: 0.9427 (mt) cc_final: 0.9147 (mt) outliers start: 21 outliers final: 13 residues processed: 174 average time/residue: 0.1428 time to fit residues: 33.4843 Evaluate side-chains 162 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 62 ILE 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 O residue 90 MET Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 105 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 94 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 0.0980 chunk 66 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.064831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.052064 restraints weight = 68056.738| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.93 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2096 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= 0.189 Angle : 0.663 8.899 19475 Z= 0.385 Chirality : 0.037 0.167 2220 Planarity : 0.005 0.062 1378 Dihedral : 34.060 179.420 4276 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.53 % Allowed : 29.11 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.30), residues: 759 helix: 1.57 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -1.64 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 92 TYR 0.042 0.002 TYR Q 88 PHE 0.014 0.001 PHE M 62 HIS 0.002 0.001 HIS M 79 Details of bonding type rmsd covalent geometry : bond 0.00427 (13413) covalent geometry : angle 0.66338 (19475) hydrogen bonds : bond 0.06485 ( 791) hydrogen bonds : angle 3.24820 ( 1919) *********************** 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 187 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 50 GLU cc_start: 0.9370 (pt0) cc_final: 0.9134 (pt0) REVERT: I 64 LYS cc_start: 0.8489 (mmmt) cc_final: 0.8226 (mmmt) REVERT: K 64 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8016 (mm-30) REVERT: K 65 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8305 (mm) REVERT: K 92 GLU cc_start: 0.9082 (pm20) cc_final: 0.8851 (pm20) REVERT: M 42 LEU cc_start: 0.9316 (pp) cc_final: 0.8907 (tp) REVERT: M 54 LYS cc_start: 0.8717 (pttm) cc_final: 0.8432 (ptpt) REVERT: M 92 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8305 (tm-30) REVERT: O 90 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8324 (tpp) REVERT: O 93 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.6886 (tt0) REVERT: Q 59 LYS cc_start: 0.8146 (mttt) cc_final: 0.7825 (mtmm) REVERT: R 84 GLN cc_start: 0.8839 (tp40) cc_final: 0.8411 (tp40) REVERT: R 118 LYS cc_start: 0.5693 (mmmm) cc_final: 0.5439 (mmmm) REVERT: S 42 LEU cc_start: 0.8656 (mt) cc_final: 0.8295 (tp) REVERT: S 68 GLU cc_start: 0.8759 (pp20) cc_final: 0.8447 (tp30) REVERT: S 103 LEU cc_start: 0.9413 (mt) cc_final: 0.9187 (mt) outliers start: 16 outliers final: 7 residues processed: 181 average time/residue: 0.1374 time to fit residues: 34.2798 Evaluate side-chains 167 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain J residue 62 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 O residue 90 MET Chi-restraints excluded: chain O residue 93 GLN Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain S residue 105 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 88 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 73 ASN M 60 ASN ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.064867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.052117 restraints weight = 69224.488| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.98 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13413 Z= 0.191 Angle : 0.662 7.414 19475 Z= 0.384 Chirality : 0.037 0.214 2220 Planarity : 0.005 0.062 1378 Dihedral : 34.019 179.514 4276 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.16 % Allowed : 29.27 % Favored : 67.56 % 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 aren not related in a simple way. whole: 1.00 (0.31), residues: 759 helix: 1.57 (0.23), residues: 531 sheet: None (None), residues: 0 loop : -1.55 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 92 TYR 0.049 0.002 TYR S 80 PHE 0.012 0.001 PHE O 67 HIS 0.002 0.001 HIS M 79 Details of bonding type rmsd covalent geometry : bond 0.00432 (13413) covalent geometry : angle 0.66244 (19475) hydrogen bonds : bond 0.06433 ( 791) hydrogen bonds : angle 3.22312 ( 1919) *********************** 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 193 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 50 GLU cc_start: 0.9341 (pt0) cc_final: 0.9112 (pt0) REVERT: I 74 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8535 (tt) REVERT: K 64 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8131 (mm-30) REVERT: K 65 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8272 (mm) REVERT: M 31 LYS cc_start: 0.8060 (ttpp) cc_final: 0.7697 (tmmt) REVERT: M 54 LYS cc_start: 0.8707 (pttm) cc_final: 0.8459 (ptmt) REVERT: M 92 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8312 (tm-30) REVERT: O 93 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.7021 (tt0) REVERT: Q 59 LYS cc_start: 0.8154 (mttt) cc_final: 0.7694 (mtmm) REVERT: Q 92 ARG cc_start: 0.8560 (ttt90) cc_final: 0.8336 (ttt90) REVERT: R 84 GLN cc_start: 0.8831 (tp40) cc_final: 0.8380 (tp40) REVERT: S 42 LEU cc_start: 0.8672 (mt) cc_final: 0.8342 (tp) REVERT: S 68 GLU cc_start: 0.8739 (pp20) cc_final: 0.8460 (tp30) outliers start: 20 outliers final: 11 residues processed: 181 average time/residue: 0.1379 time to fit residues: 34.4730 Evaluate side-chains 167 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 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 59 MET 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 Chi-restraints excluded: chain S residue 105 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 76 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 102 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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** Q 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.062204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.049594 restraints weight = 69511.313| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 3.01 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2729 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= 0.263 Angle : 0.710 6.094 19475 Z= 0.413 Chirality : 0.040 0.158 2220 Planarity : 0.005 0.063 1378 Dihedral : 34.167 179.888 4276 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.64 % Allowed : 28.80 % Favored : 67.56 % 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 aren not related in a simple way. whole: 0.66 (0.30), residues: 759 helix: 1.33 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -1.53 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Q 92 TYR 0.065 0.003 TYR S 80 PHE 0.013 0.002 PHE M 62 HIS 0.004 0.001 HIS I 113 Details of bonding type rmsd covalent geometry : bond 0.00590 (13413) covalent geometry : angle 0.70971 (19475) hydrogen bonds : bond 0.07386 ( 791) hydrogen bonds : angle 3.42903 ( 1919) *********************** 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 181 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 50 GLU cc_start: 0.9384 (pt0) cc_final: 0.9123 (pt0) REVERT: I 59 GLU cc_start: 0.7935 (pm20) cc_final: 0.7441 (pm20) REVERT: I 74 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8715 (tt) REVERT: K 61 GLU cc_start: 0.8775 (tp30) cc_final: 0.7869 (tp30) REVERT: M 31 LYS cc_start: 0.8093 (ttpp) cc_final: 0.7737 (tmmt) REVERT: M 92 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8336 (tm-30) REVERT: O 90 MET cc_start: 0.8805 (mmm) cc_final: 0.8272 (mmm) REVERT: Q 63 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8726 (mt-10) REVERT: R 84 GLN cc_start: 0.8876 (tp40) cc_final: 0.8428 (tp40) REVERT: S 68 GLU cc_start: 0.8840 (pp20) cc_final: 0.8551 (tp30) REVERT: S 76 ARG cc_start: 0.8656 (ttm110) cc_final: 0.8271 (ttm170) outliers start: 23 outliers final: 15 residues processed: 171 average time/residue: 0.1281 time to fit residues: 30.7466 Evaluate side-chains 164 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 43 VAL 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 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 Q residue 43 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain S residue 105 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 16 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 73 ASN ** K 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.064565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.051989 restraints weight = 68463.581| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.96 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2712 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= 0.185 Angle : 0.677 10.293 19475 Z= 0.392 Chirality : 0.038 0.201 2220 Planarity : 0.005 0.061 1378 Dihedral : 34.018 179.993 4276 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.16 % Allowed : 30.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.30), residues: 759 helix: 1.37 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -1.55 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 92 TYR 0.058 0.002 TYR S 80 PHE 0.008 0.001 PHE I 67 HIS 0.003 0.001 HIS Q 75 Details of bonding type rmsd covalent geometry : bond 0.00418 (13413) covalent geometry : angle 0.67682 (19475) hydrogen bonds : bond 0.06445 ( 791) hydrogen bonds : angle 3.29809 ( 1919) *********************** 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 193 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 50 GLU cc_start: 0.9322 (pt0) cc_final: 0.9111 (pt0) REVERT: I 59 GLU cc_start: 0.7805 (pm20) cc_final: 0.7331 (pm20) REVERT: I 130 ILE cc_start: 0.9158 (mt) cc_final: 0.8956 (mp) REVERT: K 65 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8263 (mm) REVERT: M 31 LYS cc_start: 0.8157 (ttpp) cc_final: 0.7912 (tmmt) REVERT: M 92 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8328 (tm-30) REVERT: O 79 LYS cc_start: 0.8692 (tptp) cc_final: 0.8484 (tptp) REVERT: Q 63 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8688 (mt-10) REVERT: R 84 GLN cc_start: 0.8827 (tp40) cc_final: 0.8370 (tp40) REVERT: S 68 GLU cc_start: 0.8758 (pp20) cc_final: 0.8463 (tp30) outliers start: 20 outliers final: 13 residues processed: 182 average time/residue: 0.1304 time to fit residues: 33.2661 Evaluate side-chains 172 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 59 LYS 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 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 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 23 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 85 optimal weight: 0.0570 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.7704 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.062930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.050419 restraints weight = 68832.076| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.98 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13413 Z= 0.234 Angle : 0.713 9.001 19475 Z= 0.411 Chirality : 0.040 0.232 2220 Planarity : 0.005 0.062 1378 Dihedral : 34.065 179.640 4276 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.16 % Allowed : 31.96 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.30), residues: 759 helix: 1.34 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -1.54 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 92 TYR 0.077 0.003 TYR S 80 PHE 0.015 0.002 PHE M 62 HIS 0.004 0.001 HIS I 113 Details of bonding type rmsd covalent geometry : bond 0.00529 (13413) covalent geometry : angle 0.71265 (19475) hydrogen bonds : bond 0.06922 ( 791) hydrogen bonds : angle 3.41761 ( 1919) *********************** 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 181 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 59 GLU cc_start: 0.7829 (pm20) cc_final: 0.7372 (pm20) REVERT: I 74 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8609 (tt) REVERT: K 65 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8331 (mm) REVERT: M 31 LYS cc_start: 0.8141 (ttpp) cc_final: 0.7898 (tmmt) REVERT: M 92 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8366 (tm-30) REVERT: O 79 LYS cc_start: 0.8726 (tptp) cc_final: 0.8421 (tptp) REVERT: Q 63 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8662 (mt-10) REVERT: R 84 GLN cc_start: 0.8836 (tp40) cc_final: 0.8373 (tp40) REVERT: S 68 GLU cc_start: 0.8777 (pp20) cc_final: 0.8445 (tp30) REVERT: S 76 ARG cc_start: 0.8483 (ttm110) cc_final: 0.8200 (ttm170) outliers start: 20 outliers final: 14 residues processed: 171 average time/residue: 0.1389 time to fit residues: 32.8997 Evaluate side-chains 171 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 59 LYS 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 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 103 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 31 LYS 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 86 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.064905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.052359 restraints weight = 68699.598| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.97 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2949 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= 0.187 Angle : 0.698 9.973 19475 Z= 0.400 Chirality : 0.039 0.217 2220 Planarity : 0.005 0.061 1378 Dihedral : 33.932 179.425 4276 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.37 % Allowed : 33.86 % Favored : 63.77 % 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 aren not related in a simple way. whole: 0.55 (0.30), residues: 759 helix: 1.31 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -1.63 (0.35), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 76 TYR 0.072 0.003 TYR S 80 PHE 0.008 0.001 PHE I 67 HIS 0.003 0.001 HIS J 75 Details of bonding type rmsd covalent geometry : bond 0.00423 (13413) covalent geometry : angle 0.69797 (19475) hydrogen bonds : bond 0.06422 ( 791) hydrogen bonds : angle 3.39767 ( 1919) *********************** 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 186 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 59 GLU cc_start: 0.7794 (pm20) cc_final: 0.7309 (pm20) REVERT: K 65 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8140 (mm) REVERT: M 31 LYS cc_start: 0.8142 (ttpp) cc_final: 0.7894 (tmmt) REVERT: M 92 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8325 (tm-30) REVERT: O 79 LYS cc_start: 0.8765 (tptp) cc_final: 0.8473 (tptp) REVERT: O 90 MET cc_start: 0.8663 (mmm) cc_final: 0.8002 (mmm) REVERT: Q 63 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8080 (mt-10) REVERT: R 84 GLN cc_start: 0.8826 (tp40) cc_final: 0.8364 (tp40) REVERT: S 68 GLU cc_start: 0.8768 (pp20) cc_final: 0.8430 (tp30) REVERT: S 76 ARG cc_start: 0.8502 (ttm110) cc_final: 0.8158 (ttm170) outliers start: 15 outliers final: 11 residues processed: 178 average time/residue: 0.1354 time to fit residues: 33.5514 Evaluate side-chains 173 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 59 LYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.060560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.048121 restraints weight = 71586.300| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.07 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 13413 Z= 0.329 Angle : 0.795 12.311 19475 Z= 0.457 Chirality : 0.044 0.298 2220 Planarity : 0.006 0.047 1378 Dihedral : 34.239 179.087 4276 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 22.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.01 % Allowed : 32.91 % Favored : 64.08 % 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 aren not related in a simple way. whole: 0.18 (0.30), residues: 759 helix: 0.99 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -1.65 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 116 TYR 0.088 0.004 TYR S 80 PHE 0.017 0.002 PHE I 67 HIS 0.007 0.002 HIS R 82 Details of bonding type rmsd covalent geometry : bond 0.00739 (13413) covalent geometry : angle 0.79545 (19475) hydrogen bonds : bond 0.08187 ( 791) hydrogen bonds : angle 3.71224 ( 1919) ********************** 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 175 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 59 GLU cc_start: 0.7974 (pm20) cc_final: 0.7497 (pm20) REVERT: I 93 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8629 (tm-30) REVERT: K 65 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8299 (mm) REVERT: M 31 LYS cc_start: 0.8158 (ttpp) cc_final: 0.7922 (tmmt) REVERT: M 92 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8273 (tm-30) REVERT: O 79 LYS cc_start: 0.8820 (tptp) cc_final: 0.8401 (tptp) REVERT: Q 63 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8152 (mt-10) REVERT: R 84 GLN cc_start: 0.8906 (tp40) cc_final: 0.8432 (tp40) REVERT: S 68 GLU cc_start: 0.8859 (pp20) cc_final: 0.8510 (tp30) REVERT: S 76 ARG cc_start: 0.8501 (ttm110) cc_final: 0.8188 (ttm170) outliers start: 19 outliers final: 12 residues processed: 166 average time/residue: 0.1344 time to fit residues: 30.5835 Evaluate side-chains 160 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain I residue 104 PHE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 102 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.064208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.051603 restraints weight = 69448.910| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.04 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 13413 Z= 0.194 Angle : 0.731 9.604 19475 Z= 0.418 Chirality : 0.040 0.213 2220 Planarity : 0.005 0.044 1378 Dihedral : 33.992 179.056 4276 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.22 % Allowed : 33.54 % Favored : 64.24 % 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 aren not related in a simple way. whole: 0.31 (0.30), residues: 759 helix: 1.07 (0.23), residues: 511 sheet: None (None), residues: 0 loop : -1.61 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 95 TYR 0.070 0.003 TYR S 80 PHE 0.014 0.001 PHE M 62 HIS 0.003 0.001 HIS R 82 Details of bonding type rmsd covalent geometry : bond 0.00447 (13413) covalent geometry : angle 0.73077 (19475) hydrogen bonds : bond 0.06605 ( 791) hydrogen bonds : angle 3.49491 ( 1919) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3203.44 seconds wall clock time: 55 minutes 38.02 seconds (3338.02 seconds total)