Starting phenix.real_space_refine on Wed Jul 30 12:45:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vob_43373/07_2025/8vob_43373.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vob_43373/07_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_43373/07_2025/8vob_43373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vob_43373/07_2025/8vob_43373.map" model { file = "/net/cci-nas-00/data/ceres_data/8vob_43373/07_2025/8vob_43373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vob_43373/07_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-5711/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: 7.29, per 1000 atoms: 0.58 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: 2.80 Conformation dependent library (CDL) restraints added in 844.8 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: 5.56 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: 4.84 Time building geometry restraints manager: 3.37 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: 3.880 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 32.480 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.060 ------------------------------------------------------------------------------- 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 : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 161 average time/residue: 0.2868 time to fit residues: 63.2395 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 : 0.996 ------------------------------------------------------------------------------- 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 = 0.3999 r_free = 0.3999 target = 0.067521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.054815 restraints weight = 67026.902| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.95 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 3.22954 ( 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 : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 37 LYS cc_start: 0.8756 (tppt) cc_final: 0.8553 (tptp) REVERT: I 50 GLU cc_start: 0.9329 (pt0) cc_final: 0.9063 (pt0) REVERT: I 64 LYS cc_start: 0.8626 (mmmt) cc_final: 0.8221 (mmmt) REVERT: J 78 ARG cc_start: 0.8163 (ptp90) cc_final: 0.7951 (ptp90) REVERT: K 64 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7987 (mm-30) REVERT: M 54 LYS cc_start: 0.8778 (pttm) cc_final: 0.8409 (ptmt) REVERT: M 92 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8313 (tm-30) REVERT: O 90 MET cc_start: 0.8442 (mpp) cc_final: 0.8063 (mmm) REVERT: Q 93 GLN cc_start: 0.8683 (mm110) cc_final: 0.8372 (mm110) REVERT: R 84 GLN cc_start: 0.8870 (tp40) cc_final: 0.8553 (tp40) REVERT: R 118 LYS cc_start: 0.5622 (mmmm) cc_final: 0.5380 (mtpp) REVERT: S 44 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8681 (mm110) REVERT: S 68 GLU cc_start: 0.8689 (pp20) cc_final: 0.8462 (tp30) outliers start: 16 outliers final: 5 residues processed: 174 average time/residue: 0.2744 time to fit residues: 66.1709 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 : 0.958 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.8980 chunk 25 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.063567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.050800 restraints weight = 69290.217| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.98 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 13413 Z= 0.258 Angle : 0.692 5.182 19475 Z= 0.403 Chirality : 0.040 0.167 2220 Planarity : 0.005 0.062 1378 Dihedral : 34.095 179.867 4276 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.16 % Allowed : 27.06 % Favored : 69.78 % 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: 0.83 (0.30), residues: 759 helix: 1.43 (0.23), residues: 517 sheet: None (None), residues: 0 loop : -1.40 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS J 75 PHE 0.012 0.002 PHE Q 100 TYR 0.051 0.003 TYR Q 88 ARG 0.005 0.001 ARG O 63 Details of bonding type rmsd hydrogen bonds : bond 0.07181 ( 791) hydrogen bonds : angle 3.35023 ( 1919) covalent geometry : bond 0.00579 (13413) covalent geometry : angle 0.69176 (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 : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 50 GLU cc_start: 0.9381 (pt0) cc_final: 0.9055 (pt0) REVERT: I 60 LEU cc_start: 0.8767 (mm) cc_final: 0.8530 (mm) REVERT: I 93 GLN cc_start: 0.8770 (tt0) cc_final: 0.8548 (tt0) REVERT: K 64 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7903 (mm-30) REVERT: K 65 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8293 (mm) REVERT: M 54 LYS cc_start: 0.8737 (pttm) cc_final: 0.8480 (ptpt) REVERT: M 92 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8310 (tm-30) REVERT: O 120 MET cc_start: 0.7487 (mmt) cc_final: 0.7247 (mmt) REVERT: R 84 GLN cc_start: 0.8877 (tp40) cc_final: 0.8492 (tp40) REVERT: S 68 GLU cc_start: 0.8792 (pp20) cc_final: 0.8443 (tp30) REVERT: S 103 LEU cc_start: 0.9428 (mt) cc_final: 0.9207 (mt) REVERT: S 105 LYS cc_start: 0.9592 (OUTLIER) cc_final: 0.9392 (ptpp) outliers start: 20 outliers final: 12 residues processed: 178 average time/residue: 0.3044 time to fit residues: 73.0634 Evaluate side-chains 159 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 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 31 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.065488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.052645 restraints weight = 67052.584| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.95 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1919 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= 0.181 Angle : 0.654 8.626 19475 Z= 0.380 Chirality : 0.037 0.150 2220 Planarity : 0.005 0.061 1378 Dihedral : 33.975 179.105 4276 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.22 % Allowed : 29.43 % 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 (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: 1.01 (0.30), residues: 759 helix: 1.61 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -1.61 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS M 79 PHE 0.010 0.001 PHE I 67 TYR 0.036 0.002 TYR Q 88 ARG 0.005 0.000 ARG Q 95 Details of bonding type rmsd hydrogen bonds : bond 0.06377 ( 791) hydrogen bonds : angle 3.19999 ( 1919) covalent geometry : bond 0.00412 (13413) covalent geometry : angle 0.65364 (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 190 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 50 GLU cc_start: 0.9325 (pt0) cc_final: 0.9091 (pt0) REVERT: I 60 LEU cc_start: 0.8598 (mm) cc_final: 0.8171 (mm) REVERT: I 64 LYS cc_start: 0.8550 (mmmt) cc_final: 0.8329 (mmmt) REVERT: I 93 GLN cc_start: 0.8742 (tt0) cc_final: 0.8409 (tt0) REVERT: K 64 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8134 (mm-30) REVERT: K 65 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8309 (mm) REVERT: K 92 GLU cc_start: 0.9085 (pm20) cc_final: 0.8874 (pm20) REVERT: M 39 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.7949 (t80) REVERT: M 42 LEU cc_start: 0.9239 (pp) cc_final: 0.8911 (tp) REVERT: M 54 LYS cc_start: 0.8687 (pttm) cc_final: 0.8384 (ptmt) REVERT: M 92 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8280 (tm-30) REVERT: O 90 MET cc_start: 0.8629 (mmm) cc_final: 0.8265 (mmm) REVERT: Q 59 LYS cc_start: 0.8173 (mttt) cc_final: 0.7798 (mtmm) REVERT: Q 93 GLN cc_start: 0.8725 (mm110) cc_final: 0.8378 (mm110) REVERT: R 84 GLN cc_start: 0.8833 (tp40) cc_final: 0.8417 (tp40) REVERT: S 42 LEU cc_start: 0.8656 (mt) cc_final: 0.8309 (tp) REVERT: S 68 GLU cc_start: 0.8749 (pp20) cc_final: 0.8440 (tp30) REVERT: S 103 LEU cc_start: 0.9403 (mt) cc_final: 0.9197 (mt) outliers start: 14 outliers final: 4 residues processed: 184 average time/residue: 0.3517 time to fit residues: 89.5339 Evaluate side-chains 164 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 157 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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: 1.9990 chunk 41 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 Q 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.063411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.050706 restraints weight = 69090.488| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.99 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13413 Z= 0.238 Angle : 0.681 6.545 19475 Z= 0.397 Chirality : 0.039 0.194 2220 Planarity : 0.005 0.063 1378 Dihedral : 34.105 179.436 4276 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.32 % Allowed : 28.80 % 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: 0.91 (0.31), residues: 759 helix: 1.53 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -1.63 (0.37), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS M 79 PHE 0.016 0.002 PHE O 67 TYR 0.052 0.002 TYR S 80 ARG 0.004 0.000 ARG Q 92 Details of bonding type rmsd hydrogen bonds : bond 0.06924 ( 791) hydrogen bonds : angle 3.32825 ( 1919) covalent geometry : bond 0.00536 (13413) covalent geometry : angle 0.68141 (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 189 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 60 LEU cc_start: 0.8740 (mm) cc_final: 0.8433 (mm) REVERT: I 64 LYS cc_start: 0.8450 (mmmt) cc_final: 0.8149 (mmmt) REVERT: I 93 GLN cc_start: 0.8829 (tt0) cc_final: 0.8331 (tt0) REVERT: J 53 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8785 (pt0) REVERT: K 61 GLU cc_start: 0.8596 (tp30) cc_final: 0.7446 (tp30) REVERT: K 65 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8350 (mm) REVERT: M 54 LYS cc_start: 0.8754 (pttm) cc_final: 0.8518 (ptmt) REVERT: M 92 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8336 (tm-30) REVERT: O 90 MET cc_start: 0.8747 (mmm) cc_final: 0.8350 (mmm) REVERT: O 93 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.6885 (tt0) REVERT: Q 82 THR cc_start: 0.7749 (p) cc_final: 0.7540 (p) REVERT: Q 93 GLN cc_start: 0.8807 (mm110) cc_final: 0.8601 (mm110) REVERT: R 84 GLN cc_start: 0.8875 (tp40) cc_final: 0.8436 (tp40) REVERT: S 68 GLU cc_start: 0.8771 (pp20) cc_final: 0.8484 (tp30) outliers start: 21 outliers final: 10 residues processed: 177 average time/residue: 0.2789 time to fit residues: 67.8150 Evaluate side-chains 165 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 51 LEU Chi-restraints excluded: chain K residue 65 LEU 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 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: 3.9990 chunk 53 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 73 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 = 0.3921 r_free = 0.3921 target = 0.064248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.051669 restraints weight = 69206.946| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.99 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2479 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 : 0.680 10.098 19475 Z= 0.394 Chirality : 0.038 0.174 2220 Planarity : 0.005 0.062 1378 Dihedral : 34.035 179.758 4276 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.16 % Allowed : 29.91 % Favored : 66.93 % 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: 0.83 (0.30), residues: 759 helix: 1.51 (0.23), residues: 527 sheet: None (None), residues: 0 loop : -1.74 (0.36), residues: 232 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 0.066 0.002 TYR S 80 ARG 0.006 0.000 ARG S 76 Details of bonding type rmsd hydrogen bonds : bond 0.06527 ( 791) hydrogen bonds : angle 3.31930 ( 1919) covalent geometry : bond 0.00457 (13413) covalent geometry : angle 0.67963 (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: 20 poor density : 166 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 59 GLU cc_start: 0.7917 (pm20) cc_final: 0.7687 (pm20) REVERT: I 74 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8580 (tt) REVERT: K 65 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8202 (mm) REVERT: K 92 GLU cc_start: 0.9069 (pm20) cc_final: 0.8855 (pm20) REVERT: M 42 LEU cc_start: 0.9253 (pp) cc_final: 0.8812 (tp) REVERT: M 54 LYS cc_start: 0.8703 (pttm) cc_final: 0.8466 (ptmt) REVERT: M 92 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8324 (tm-30) REVERT: O 90 MET cc_start: 0.8689 (mmm) cc_final: 0.8346 (mmm) REVERT: O 93 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.6811 (tt0) REVERT: Q 59 LYS cc_start: 0.8333 (mttt) cc_final: 0.7853 (mtmm) REVERT: Q 93 GLN cc_start: 0.8761 (mm110) cc_final: 0.8528 (mm110) REVERT: R 84 GLN cc_start: 0.8850 (tp40) cc_final: 0.8395 (tp40) REVERT: S 68 GLU cc_start: 0.8747 (pp20) cc_final: 0.8439 (tp30) REVERT: S 76 ARG cc_start: 0.8617 (ttm110) cc_final: 0.8248 (ttm170) outliers start: 20 outliers final: 11 residues processed: 175 average time/residue: 0.3043 time to fit residues: 74.0672 Evaluate side-chains 165 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 85 optimal weight: 0.0870 chunk 9 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 68 optimal weight: 0.0570 chunk 80 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.8282 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.063052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.050436 restraints weight = 69083.896| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.99 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2725 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= 0.233 Angle : 0.696 7.859 19475 Z= 0.403 Chirality : 0.039 0.217 2220 Planarity : 0.005 0.062 1378 Dihedral : 34.082 179.953 4276 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.32 % Allowed : 30.70 % Favored : 65.98 % 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: 0.91 (0.31), residues: 759 helix: 1.53 (0.23), residues: 525 sheet: None (None), residues: 0 loop : -1.57 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 113 PHE 0.012 0.001 PHE I 67 TYR 0.053 0.002 TYR S 80 ARG 0.005 0.000 ARG Q 92 Details of bonding type rmsd hydrogen bonds : bond 0.06874 ( 791) hydrogen bonds : angle 3.37841 ( 1919) covalent geometry : bond 0.00527 (13413) covalent geometry : angle 0.69636 (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 181 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 59 GLU cc_start: 0.7898 (pm20) cc_final: 0.7419 (pm20) REVERT: I 74 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8711 (tt) REVERT: K 65 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8220 (mm) REVERT: M 42 LEU cc_start: 0.9284 (pp) cc_final: 0.8941 (tp) REVERT: M 54 LYS cc_start: 0.8701 (pttm) cc_final: 0.8464 (ptmt) REVERT: M 92 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8345 (tm-30) REVERT: O 90 MET cc_start: 0.8725 (mmm) cc_final: 0.8407 (mmm) REVERT: O 93 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.6741 (tt0) REVERT: Q 59 LYS cc_start: 0.8382 (mttt) cc_final: 0.7830 (mtmm) REVERT: Q 63 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8707 (mt-10) REVERT: R 84 GLN cc_start: 0.8866 (tp40) cc_final: 0.8406 (tp40) REVERT: S 42 LEU cc_start: 0.8649 (mt) cc_final: 0.8237 (tp) REVERT: S 68 GLU cc_start: 0.8777 (pp20) cc_final: 0.8448 (tp30) REVERT: S 76 ARG cc_start: 0.8616 (ttm110) cc_final: 0.8194 (ttm170) REVERT: S 105 LYS cc_start: 0.9569 (OUTLIER) cc_final: 0.9346 (mtmm) outliers start: 21 outliers final: 13 residues processed: 171 average time/residue: 0.2668 time to fit residues: 63.5184 Evaluate side-chains 170 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 ILE 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 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 Q residue 96 THR Chi-restraints excluded: chain R residue 16 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 70 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 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: 0.5980 chunk 51 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3926 r_free = 0.3926 target = 0.064354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.051766 restraints weight = 68904.791| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.99 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 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 : 0.004 0.054 13413 Z= 0.193 Angle : 0.688 8.482 19475 Z= 0.397 Chirality : 0.039 0.196 2220 Planarity : 0.005 0.061 1378 Dihedral : 34.004 179.947 4276 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.37 % Allowed : 32.75 % 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 (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: 0.82 (0.30), residues: 759 helix: 1.47 (0.23), residues: 513 sheet: None (None), residues: 0 loop : -1.49 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 113 PHE 0.015 0.001 PHE M 62 TYR 0.044 0.002 TYR S 80 ARG 0.004 0.000 ARG Q 92 Details of bonding type rmsd hydrogen bonds : bond 0.06467 ( 791) hydrogen bonds : angle 3.34624 ( 1919) covalent geometry : bond 0.00439 (13413) covalent geometry : angle 0.68838 (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: 15 poor density : 169 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 59 GLU cc_start: 0.7789 (pm20) cc_final: 0.7329 (pm20) REVERT: I 130 ILE cc_start: 0.9160 (mt) cc_final: 0.8958 (mp) REVERT: K 65 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8246 (mm) REVERT: K 73 ASN cc_start: 0.9101 (t160) cc_final: 0.8853 (t0) REVERT: M 54 LYS cc_start: 0.8603 (pttm) cc_final: 0.8333 (ptmt) REVERT: M 92 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8328 (tm-30) REVERT: O 90 MET cc_start: 0.8706 (mmm) cc_final: 0.8398 (mmm) REVERT: Q 59 LYS cc_start: 0.8356 (mttt) cc_final: 0.7755 (mppt) REVERT: Q 63 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8691 (mt-10) REVERT: Q 82 THR cc_start: 0.7607 (p) cc_final: 0.7392 (p) REVERT: R 57 TYR cc_start: 0.8384 (t80) cc_final: 0.8179 (t80) REVERT: R 84 GLN cc_start: 0.8845 (tp40) cc_final: 0.8379 (tp40) REVERT: S 68 GLU cc_start: 0.8755 (pp20) cc_final: 0.8465 (tp30) REVERT: S 105 LYS cc_start: 0.9579 (OUTLIER) cc_final: 0.9343 (mtmm) outliers start: 15 outliers final: 10 residues processed: 177 average time/residue: 0.2662 time to fit residues: 65.5233 Evaluate side-chains 168 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 26 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3945 r_free = 0.3945 target = 0.065029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.052479 restraints weight = 68234.793| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.96 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2828 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= 0.186 Angle : 0.697 10.875 19475 Z= 0.398 Chirality : 0.039 0.220 2220 Planarity : 0.005 0.061 1378 Dihedral : 33.955 179.658 4276 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.53 % Allowed : 33.07 % Favored : 64.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.44 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -1.54 (0.35), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 75 PHE 0.007 0.001 PHE I 67 TYR 0.066 0.002 TYR Q 88 ARG 0.006 0.000 ARG S 76 Details of bonding type rmsd hydrogen bonds : bond 0.06395 ( 791) hydrogen bonds : angle 3.43135 ( 1919) covalent geometry : bond 0.00423 (13413) covalent geometry : angle 0.69674 (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 183 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 59 GLU cc_start: 0.7726 (pm20) cc_final: 0.7316 (pm20) REVERT: I 126 LEU cc_start: 0.9388 (tp) cc_final: 0.9104 (tp) REVERT: I 130 ILE cc_start: 0.9153 (mt) cc_final: 0.8867 (mp) REVERT: K 61 GLU cc_start: 0.8475 (tp30) cc_final: 0.8129 (tp30) REVERT: K 64 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8216 (mp0) REVERT: K 73 ASN cc_start: 0.9115 (t160) cc_final: 0.8809 (t0) REVERT: M 54 LYS cc_start: 0.8569 (pttm) cc_final: 0.8294 (ptmt) REVERT: M 92 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8468 (tm-30) REVERT: O 90 MET cc_start: 0.8695 (mmm) cc_final: 0.8393 (mmm) REVERT: Q 63 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8633 (mt-10) REVERT: R 84 GLN cc_start: 0.8821 (tp40) cc_final: 0.8343 (tp40) REVERT: S 68 GLU cc_start: 0.8762 (pp20) cc_final: 0.8483 (tp30) REVERT: S 102 GLU cc_start: 0.8857 (pt0) cc_final: 0.8584 (pp20) REVERT: S 105 LYS cc_start: 0.9567 (OUTLIER) cc_final: 0.9323 (mtmm) outliers start: 16 outliers final: 13 residues processed: 175 average time/residue: 0.2785 time to fit residues: 67.4012 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 : 0.871 ------------------------------------------------------------------------------- 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 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 Q residue 43 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 88 TYR Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain R residue 16 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 49 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 46 optimal weight: 0.4980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.064995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.052410 restraints weight = 67835.925| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.02 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2935 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= 0.194 Angle : 0.712 9.422 19475 Z= 0.405 Chirality : 0.039 0.202 2220 Planarity : 0.005 0.060 1378 Dihedral : 33.915 179.365 4276 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.53 % Allowed : 33.23 % 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 (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: 0.67 (0.30), residues: 759 helix: 1.41 (0.23), residues: 507 sheet: None (None), residues: 0 loop : -1.59 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 113 PHE 0.016 0.001 PHE M 62 TYR 0.076 0.003 TYR Q 88 ARG 0.005 0.000 ARG Q 92 Details of bonding type rmsd hydrogen bonds : bond 0.06452 ( 791) hydrogen bonds : angle 3.45523 ( 1919) covalent geometry : bond 0.00442 (13413) covalent geometry : angle 0.71207 (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 179 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 59 GLU cc_start: 0.7705 (pm20) cc_final: 0.7292 (pm20) REVERT: I 120 MET cc_start: 0.7259 (mtt) cc_final: 0.6998 (mtp) REVERT: I 130 ILE cc_start: 0.9168 (mt) cc_final: 0.8958 (mp) REVERT: J 78 ARG cc_start: 0.8135 (ptp90) cc_final: 0.7836 (ptp90) REVERT: K 61 GLU cc_start: 0.8446 (tp30) cc_final: 0.8144 (tp30) REVERT: K 64 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8220 (mp0) REVERT: K 73 ASN cc_start: 0.9102 (t160) cc_final: 0.8818 (t0) REVERT: M 54 LYS cc_start: 0.8645 (pttm) cc_final: 0.8391 (ptmt) REVERT: M 89 ARG cc_start: 0.9015 (ttp80) cc_final: 0.8617 (ttp80) REVERT: M 92 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8477 (tm-30) REVERT: O 90 MET cc_start: 0.8754 (mmm) cc_final: 0.8435 (mmm) REVERT: Q 59 LYS cc_start: 0.8355 (mttt) cc_final: 0.7707 (mppt) REVERT: Q 63 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8658 (mt-10) REVERT: R 84 GLN cc_start: 0.8822 (tp40) cc_final: 0.8352 (tp40) REVERT: S 68 GLU cc_start: 0.8800 (pp20) cc_final: 0.8498 (tp30) REVERT: S 105 LYS cc_start: 0.9574 (OUTLIER) cc_final: 0.9343 (mtmm) outliers start: 16 outliers final: 13 residues processed: 170 average time/residue: 0.2944 time to fit residues: 69.5535 Evaluate side-chains 171 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 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 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 113 SER 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 91 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 50 optimal weight: 0.0270 overall best weight: 1.1242 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.065033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.052237 restraints weight = 68819.428| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 3.06 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3056 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= 0.197 Angle : 0.717 10.643 19475 Z= 0.407 Chirality : 0.039 0.211 2220 Planarity : 0.005 0.045 1378 Dihedral : 33.882 179.319 4276 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.69 % Allowed : 33.23 % 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 (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: 0.62 (0.30), residues: 759 helix: 1.37 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -1.59 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS R 82 PHE 0.021 0.002 PHE O 67 TYR 0.094 0.004 TYR Q 88 ARG 0.010 0.000 ARG S 76 Details of bonding type rmsd hydrogen bonds : bond 0.06482 ( 791) hydrogen bonds : angle 3.49423 ( 1919) covalent geometry : bond 0.00448 (13413) covalent geometry : angle 0.71703 (19475) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7011.98 seconds wall clock time: 122 minutes 27.56 seconds (7347.56 seconds total)