Starting phenix.real_space_refine on Wed Sep 17 23:39:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vmj_43358/09_2025/8vmj_43358.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vmj_43358/09_2025/8vmj_43358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vmj_43358/09_2025/8vmj_43358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vmj_43358/09_2025/8vmj_43358.map" model { file = "/net/cci-nas-00/data/ceres_data/8vmj_43358/09_2025/8vmj_43358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vmj_43358/09_2025/8vmj_43358.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 314 5.49 5 S 14 5.16 5 C 6889 2.51 5 N 2355 2.21 5 O 2968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12540 Number of models: 1 Model: "" Number of chains: 10 Chain: "H" Number of atoms: 3237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3237 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Chain: "I" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "J" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "K" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 736 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "O" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "Q" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 667 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "R" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "S" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 3202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3202 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Time building chain proxies: 3.05, per 1000 atoms: 0.24 Number of scatterers: 12540 At special positions: 0 Unit cell: (106.05, 141.75, 121.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 314 15.00 O 2968 8.00 N 2355 7.00 C 6889 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 355.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 69.7% alpha, 2.6% beta 157 base pairs and 269 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'I' and resid 45 through 57 Processing helix chain 'I' and resid 63 through 77 removed outlier: 3.898A pdb=" N ASP I 77 " --> pdb=" O GLU I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 114 removed outlier: 3.614A pdb=" N MET I 90 " --> pdb=" O SER I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 132 Processing helix chain 'J' and resid 30 through 42 Processing helix chain 'J' and resid 49 through 76 removed outlier: 3.554A pdb=" N GLU J 53 " --> pdb=" O LEU J 49 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG J 55 " --> pdb=" O TYR J 51 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP J 68 " --> pdb=" O ASN J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 94 Processing helix chain 'K' and resid 16 through 21 removed outlier: 3.559A pdb=" N ARG K 20 " --> pdb=" O THR K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 37 Processing helix chain 'K' and resid 45 through 73 removed outlier: 4.348A pdb=" N VAL K 49 " --> pdb=" O ALA K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 90 removed outlier: 3.660A pdb=" N ASP K 90 " --> pdb=" O ALA K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 97 removed outlier: 3.521A pdb=" N LEU K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 46 Processing helix chain 'M' and resid 52 through 81 removed outlier: 3.503A pdb=" N ASN M 81 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 99 Processing helix chain 'M' and resid 101 through 121 removed outlier: 3.742A pdb=" N SER M 109 " --> pdb=" O LYS M 105 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA M 121 " --> pdb=" O LYS M 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 57 Processing helix chain 'O' and resid 63 through 75 Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 131 Processing helix chain 'Q' and resid 25 through 29 Processing helix chain 'Q' and resid 30 through 42 Processing helix chain 'Q' and resid 49 through 77 removed outlier: 4.098A pdb=" N GLU Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP Q 68 " --> pdb=" O ASN Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 93 Processing helix chain 'R' and resid 16 through 22 removed outlier: 3.831A pdb=" N ARG R 20 " --> pdb=" O THR R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 37 Processing helix chain 'R' and resid 46 through 73 Processing helix chain 'R' and resid 79 through 90 removed outlier: 3.543A pdb=" N ASP R 90 " --> pdb=" O ALA R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 97 Processing helix chain 'S' and resid 34 through 46 Processing helix chain 'S' and resid 52 through 81 Processing helix chain 'S' and resid 87 through 99 Processing helix chain 'S' and resid 101 through 121 removed outlier: 3.617A pdb=" N LYS S 105 " --> pdb=" O GLY S 101 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA S 121 " --> pdb=" O LYS S 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 83 through 84 removed outlier: 7.168A pdb=" N ARG I 83 " --> pdb=" O VAL J 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'I' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'J' and resid 96 through 98 removed outlier: 6.151A pdb=" N THR J 96 " --> pdb=" O THR R 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'K' and resid 42 through 43 removed outlier: 7.369A pdb=" N ARG K 42 " --> pdb=" O ILE M 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'K' and resid 100 through 102 removed outlier: 6.928A pdb=" N THR K 101 " --> pdb=" O TYR Q 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.754A pdb=" N ARG O 83 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'R' and resid 42 through 43 removed outlier: 7.383A pdb=" N ARG R 42 " --> pdb=" O ILE S 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'R' and resid 77 through 78 394 hydrogen bonds defined for protein. 1176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 398 hydrogen bonds 756 hydrogen bond angles 0 basepair planarities 157 basepair parallelities 269 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1728 1.33 - 1.45: 4924 1.45 - 1.57: 6098 1.57 - 1.69: 629 1.69 - 1.82: 24 Bond restraints: 13403 Sorted by residual: bond pdb=" CG PRO O 38 " pdb=" CD PRO O 38 " ideal model delta sigma weight residual 1.503 1.205 0.298 3.40e-02 8.65e+02 7.70e+01 bond pdb=" N PRO O 38 " pdb=" CD PRO O 38 " ideal model delta sigma weight residual 1.473 1.558 -0.085 1.40e-02 5.10e+03 3.71e+01 bond pdb=" CB PRO O 38 " pdb=" CG PRO O 38 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.26e+00 bond pdb=" CB PRO I 43 " pdb=" CG PRO I 43 " ideal model delta sigma weight residual 1.492 1.617 -0.125 5.00e-02 4.00e+02 6.28e+00 bond pdb=" CE LYS M 105 " pdb=" NZ LYS M 105 " ideal model delta sigma weight residual 1.489 1.431 0.058 3.00e-02 1.11e+03 3.68e+00 ... (remaining 13398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 19397 3.79 - 7.58: 56 7.58 - 11.37: 1 11.37 - 15.16: 4 15.16 - 18.95: 1 Bond angle restraints: 19459 Sorted by residual: angle pdb=" CA PRO O 38 " pdb=" N PRO O 38 " pdb=" CD PRO O 38 " ideal model delta sigma weight residual 112.00 93.05 18.95 1.40e+00 5.10e-01 1.83e+02 angle pdb=" N PRO O 38 " pdb=" CD PRO O 38 " pdb=" CG PRO O 38 " ideal model delta sigma weight residual 103.20 88.45 14.75 1.50e+00 4.44e-01 9.67e+01 angle pdb=" CA PRO I 43 " pdb=" N PRO I 43 " pdb=" CD PRO I 43 " ideal model delta sigma weight residual 112.00 98.62 13.38 1.40e+00 5.10e-01 9.13e+01 angle pdb=" CA PRO O 38 " pdb=" CB PRO O 38 " pdb=" CG PRO O 38 " ideal model delta sigma weight residual 104.50 91.98 12.52 1.90e+00 2.77e-01 4.34e+01 angle pdb=" N VAL O 117 " pdb=" CA VAL O 117 " pdb=" C VAL O 117 " ideal model delta sigma weight residual 111.81 108.16 3.65 8.60e-01 1.35e+00 1.80e+01 ... (remaining 19454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 5729 35.91 - 71.82: 1433 71.82 - 107.73: 28 107.73 - 143.65: 8 143.65 - 179.56: 24 Dihedral angle restraints: 7222 sinusoidal: 4972 harmonic: 2250 Sorted by residual: dihedral pdb=" CA PHE R 25 " pdb=" C PHE R 25 " pdb=" N PRO R 26 " pdb=" CA PRO R 26 " ideal model delta harmonic sigma weight residual -180.00 -159.37 -20.63 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA HIS S 79 " pdb=" C HIS S 79 " pdb=" N TYR S 80 " pdb=" CA TYR S 80 " ideal model delta harmonic sigma weight residual -180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C4' DT D 68 " pdb=" C3' DT D 68 " pdb=" O3' DT D 68 " pdb=" P DT D 69 " ideal model delta sinusoidal sigma weight residual 220.00 40.44 179.56 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 7219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1825 0.049 - 0.098: 336 0.098 - 0.146: 49 0.146 - 0.195: 7 0.195 - 0.244: 1 Chirality restraints: 2218 Sorted by residual: chirality pdb=" CB THR S 112 " pdb=" CA THR S 112 " pdb=" OG1 THR S 112 " pdb=" CG2 THR S 112 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA ASN R 38 " pdb=" N ASN R 38 " pdb=" C ASN R 38 " pdb=" CB ASN R 38 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.89e-01 chirality pdb=" P DC D 93 " pdb=" OP1 DC D 93 " pdb=" OP2 DC D 93 " pdb=" O5' DC D 93 " both_signs ideal model delta sigma weight residual True 2.35 -2.52 -0.18 2.00e-01 2.50e+01 7.92e-01 ... (remaining 2215 not shown) Planarity restraints: 1377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG I 42 " 0.116 5.00e-02 4.00e+02 1.64e-01 4.29e+01 pdb=" N PRO I 43 " -0.283 5.00e-02 4.00e+02 pdb=" CA PRO I 43 " 0.083 5.00e-02 4.00e+02 pdb=" CD PRO I 43 " 0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS O 37 " 0.082 5.00e-02 4.00e+02 1.09e-01 1.90e+01 pdb=" N PRO O 38 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO O 38 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO O 38 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 80 " 0.031 2.00e-02 2.50e+03 2.66e-02 1.42e+01 pdb=" CG TYR S 80 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR S 80 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR S 80 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR S 80 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR S 80 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR S 80 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR S 80 " 0.001 2.00e-02 2.50e+03 ... (remaining 1374 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 268 2.65 - 3.21: 10562 3.21 - 3.77: 24047 3.77 - 4.34: 30514 4.34 - 4.90: 43251 Nonbonded interactions: 108642 Sorted by model distance: nonbonded pdb=" O2 DC H 110 " pdb=" N2 DG D 48 " model vdw 2.082 2.496 nonbonded pdb=" N2 DG H 137 " pdb=" O2 DC D 21 " model vdw 2.097 2.496 nonbonded pdb=" OD2 ASP M 65 " pdb=" OH TYR Q 98 " model vdw 2.101 3.040 nonbonded pdb=" N2 DG H 94 " pdb=" O2 DC D 64 " model vdw 2.110 2.496 nonbonded pdb=" O2 DC H 154 " pdb=" N2 DG D 4 " model vdw 2.125 2.496 ... (remaining 108637 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'I' and resid 37 through 135) selection = chain 'O' } ncs_group { reference = (chain 'J' and ((resid 20 through 23 and (name N or name CA or name C or name O \ or name CB )) or resid 24 through 102)) selection = (chain 'Q' and resid 20 through 102) } ncs_group { reference = chain 'K' selection = (chain 'R' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 119)) } ncs_group { reference = chain 'M' selection = (chain 'S' and resid 28 through 122) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.620 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 14.090 Find NCS groups from input model: 0.080 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 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 : 0.006 0.298 13403 Z= 0.225 Angle : 0.743 18.945 19459 Z= 0.437 Chirality : 0.039 0.244 2218 Planarity : 0.008 0.164 1377 Dihedral : 31.124 179.557 5770 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.63 % Allowed : 23.58 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.30), residues: 760 helix: 1.06 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.11 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 40 TYR 0.064 0.003 TYR S 80 PHE 0.022 0.003 PHE R 25 HIS 0.011 0.002 HIS R 31 Details of bonding type rmsd covalent geometry : bond 0.00557 (13403) covalent geometry : angle 0.74269 (19459) hydrogen bonds : bond 0.10030 ( 792) hydrogen bonds : angle 4.07596 ( 1932) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: S 102 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7220 (tm-30) outliers start: 4 outliers final: 3 residues processed: 129 average time/residue: 0.1673 time to fit residues: 28.8528 Evaluate side-chains 124 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 121 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain R residue 25 PHE Chi-restraints excluded: chain S residue 49 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0070 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 38 ASN M 60 ASN ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 GLN O 125 GLN ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 ASN S 81 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.184076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.138279 restraints weight = 20688.798| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 1.55 r_work: 0.3736 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 13403 Z= 0.187 Angle : 0.649 6.962 19459 Z= 0.374 Chirality : 0.038 0.160 2218 Planarity : 0.005 0.068 1377 Dihedral : 33.447 179.292 4275 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.11 % Allowed : 21.04 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.29), residues: 760 helix: 1.49 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -1.12 (0.39), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 83 TYR 0.047 0.002 TYR S 80 PHE 0.013 0.002 PHE O 104 HIS 0.005 0.001 HIS S 79 Details of bonding type rmsd covalent geometry : bond 0.00430 (13403) covalent geometry : angle 0.64940 (19459) hydrogen bonds : bond 0.07094 ( 792) hydrogen bonds : angle 3.25497 ( 1932) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: K 25 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7798 (t80) REVERT: M 48 ASP cc_start: 0.8262 (p0) cc_final: 0.8025 (p0) REVERT: O 59 GLU cc_start: 0.7618 (pp20) cc_final: 0.7373 (pp20) REVERT: Q 77 LYS cc_start: 0.7893 (mmmt) cc_final: 0.7643 (mmmt) REVERT: Q 85 ASP cc_start: 0.8468 (m-30) cc_final: 0.8218 (m-30) REVERT: R 74 LYS cc_start: 0.8537 (mmtt) cc_final: 0.8307 (mmtt) outliers start: 26 outliers final: 17 residues processed: 149 average time/residue: 0.1702 time to fit residues: 33.3134 Evaluate side-chains 146 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 90 MET Chi-restraints excluded: chain R residue 24 GLN Chi-restraints excluded: chain R residue 25 PHE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 97 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 79 optimal weight: 0.0870 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- 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 81 ASN O 108 ASN ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 GLN ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.166497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.119643 restraints weight = 20286.806| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.55 r_work: 0.3490 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13403 Z= 0.269 Angle : 0.765 11.361 19459 Z= 0.431 Chirality : 0.043 0.205 2218 Planarity : 0.006 0.054 1377 Dihedral : 33.809 178.143 4273 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 7.59 % Allowed : 18.20 % Favored : 74.21 % 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: 0.52 (0.29), residues: 760 helix: 1.00 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -1.23 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 129 TYR 0.065 0.003 TYR S 80 PHE 0.022 0.003 PHE M 67 HIS 0.010 0.002 HIS O 113 Details of bonding type rmsd covalent geometry : bond 0.00621 (13403) covalent geometry : angle 0.76524 (19459) hydrogen bonds : bond 0.07400 ( 792) hydrogen bonds : angle 3.66384 ( 1932) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 144 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: I 125 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8472 (mt0) REVERT: J 91 LYS cc_start: 0.9017 (ttpp) cc_final: 0.8634 (ttpp) REVERT: K 25 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.7563 (t80) REVERT: K 36 LYS cc_start: 0.8918 (mmtm) cc_final: 0.8690 (mttm) REVERT: M 32 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7944 (mt-10) REVERT: M 96 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7556 (mpp80) REVERT: Q 77 LYS cc_start: 0.8035 (mmmt) cc_final: 0.7717 (mmmt) outliers start: 48 outliers final: 23 residues processed: 174 average time/residue: 0.1720 time to fit residues: 39.1179 Evaluate side-chains 152 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain I residue 125 GLN Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 96 ARG Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain Q residue 91 LYS Chi-restraints excluded: chain R residue 24 GLN Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 97 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 10 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 54 optimal weight: 0.0980 chunk 60 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 81 ASN ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.168090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.122046 restraints weight = 20077.673| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.53 r_work: 0.3526 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13403 Z= 0.189 Angle : 0.648 6.628 19459 Z= 0.376 Chirality : 0.038 0.185 2218 Planarity : 0.005 0.048 1377 Dihedral : 33.566 179.073 4271 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.59 % Allowed : 19.78 % Favored : 75.63 % 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: 1.09 (0.29), residues: 760 helix: 1.43 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -1.07 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 30 TYR 0.060 0.002 TYR S 80 PHE 0.012 0.002 PHE O 67 HIS 0.003 0.001 HIS R 31 Details of bonding type rmsd covalent geometry : bond 0.00431 (13403) covalent geometry : angle 0.64799 (19459) hydrogen bonds : bond 0.06720 ( 792) hydrogen bonds : angle 3.20082 ( 1932) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.278 Fit side-chains REVERT: I 125 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8319 (mt0) REVERT: J 84 MET cc_start: 0.7831 (mmm) cc_final: 0.7598 (mmt) REVERT: K 25 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.7429 (t80) REVERT: M 30 ARG cc_start: 0.7409 (ptm160) cc_final: 0.7181 (ptm160) REVERT: Q 77 LYS cc_start: 0.7956 (mmmt) cc_final: 0.7593 (mmmt) REVERT: Q 84 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7993 (mpp) outliers start: 29 outliers final: 21 residues processed: 155 average time/residue: 0.1749 time to fit residues: 35.3506 Evaluate side-chains 152 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain I residue 125 GLN Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 84 MET Chi-restraints excluded: chain R residue 24 GLN Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 97 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 44 optimal weight: 0.0980 chunk 62 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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** ** K 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.163899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.117953 restraints weight = 19916.936| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.50 r_work: 0.3467 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13403 Z= 0.225 Angle : 0.683 6.494 19459 Z= 0.391 Chirality : 0.040 0.179 2218 Planarity : 0.005 0.045 1377 Dihedral : 33.638 179.027 4271 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.85 % Allowed : 20.25 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.29), residues: 760 helix: 1.48 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -1.03 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 32 TYR 0.059 0.002 TYR S 80 PHE 0.013 0.002 PHE I 67 HIS 0.005 0.001 HIS O 113 Details of bonding type rmsd covalent geometry : bond 0.00517 (13403) covalent geometry : angle 0.68279 (19459) hydrogen bonds : bond 0.06750 ( 792) hydrogen bonds : angle 3.25871 ( 1932) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.353 Fit side-chains REVERT: J 84 MET cc_start: 0.7821 (mmm) cc_final: 0.7575 (mmt) REVERT: J 91 LYS cc_start: 0.9018 (ttpp) cc_final: 0.8666 (ttpp) REVERT: K 25 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.7608 (t80) REVERT: M 32 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7986 (mt-10) REVERT: M 85 THR cc_start: 0.8250 (OUTLIER) cc_final: 0.7956 (m) REVERT: M 90 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7470 (mp0) REVERT: O 49 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7912 (ttm170) REVERT: Q 77 LYS cc_start: 0.8132 (mmmt) cc_final: 0.7813 (mmmt) outliers start: 37 outliers final: 24 residues processed: 150 average time/residue: 0.1726 time to fit residues: 34.1024 Evaluate side-chains 150 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain R residue 24 GLN Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 76 ARG Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 2 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 36 optimal weight: 0.0870 chunk 56 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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** ** K 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.161796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.115718 restraints weight = 19881.065| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.61 r_work: 0.3404 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.5747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13403 Z= 0.213 Angle : 0.658 6.638 19459 Z= 0.379 Chirality : 0.039 0.175 2218 Planarity : 0.004 0.044 1377 Dihedral : 33.576 178.666 4271 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.27 % Allowed : 21.99 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.29), residues: 760 helix: 1.62 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.96 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 30 TYR 0.057 0.002 TYR S 80 PHE 0.012 0.002 PHE O 67 HIS 0.004 0.001 HIS I 113 Details of bonding type rmsd covalent geometry : bond 0.00489 (13403) covalent geometry : angle 0.65801 (19459) hydrogen bonds : bond 0.06702 ( 792) hydrogen bonds : angle 3.16365 ( 1932) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.359 Fit side-chains REVERT: K 25 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.7531 (t80) REVERT: M 106 HIS cc_start: 0.8454 (OUTLIER) cc_final: 0.8203 (m170) REVERT: Q 77 LYS cc_start: 0.8066 (mmmt) cc_final: 0.7717 (mmmt) outliers start: 27 outliers final: 23 residues processed: 144 average time/residue: 0.1668 time to fit residues: 31.8645 Evaluate side-chains 147 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 106 HIS Chi-restraints excluded: chain Q residue 25 ASN Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 37 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 48 optimal weight: 0.0770 chunk 59 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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** ** K 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.162606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.116627 restraints weight = 19786.687| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.60 r_work: 0.3425 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13403 Z= 0.185 Angle : 0.643 5.892 19459 Z= 0.372 Chirality : 0.038 0.181 2218 Planarity : 0.004 0.044 1377 Dihedral : 33.465 179.710 4271 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.91 % Allowed : 21.68 % Favored : 73.42 % 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: 1.59 (0.29), residues: 760 helix: 1.81 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.88 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 30 TYR 0.052 0.002 TYR S 80 PHE 0.014 0.002 PHE J 100 HIS 0.009 0.001 HIS O 39 Details of bonding type rmsd covalent geometry : bond 0.00423 (13403) covalent geometry : angle 0.64280 (19459) hydrogen bonds : bond 0.06549 ( 792) hydrogen bonds : angle 3.06993 ( 1932) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 91 LYS cc_start: 0.9051 (ttpp) cc_final: 0.8825 (ttpp) REVERT: K 25 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.7304 (t80) REVERT: M 37 TYR cc_start: 0.8633 (m-80) cc_final: 0.8226 (m-10) REVERT: M 90 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: M 96 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7584 (mpp80) REVERT: M 106 HIS cc_start: 0.8482 (OUTLIER) cc_final: 0.8195 (m170) REVERT: O 90 MET cc_start: 0.7937 (mmp) cc_final: 0.7674 (mmm) REVERT: Q 77 LYS cc_start: 0.8054 (mmmt) cc_final: 0.7713 (mmmt) outliers start: 31 outliers final: 24 residues processed: 154 average time/residue: 0.1731 time to fit residues: 35.2251 Evaluate side-chains 155 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain M residue 96 ARG Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 106 HIS Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain Q residue 25 ASN Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 97 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 80 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 chunk 27 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 41 optimal weight: 0.0670 chunk 86 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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** ** K 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.163237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.117590 restraints weight = 19745.226| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.61 r_work: 0.3434 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.6110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13403 Z= 0.184 Angle : 0.647 10.101 19459 Z= 0.372 Chirality : 0.038 0.186 2218 Planarity : 0.004 0.044 1377 Dihedral : 33.403 179.497 4271 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 5.38 % Allowed : 21.68 % Favored : 72.94 % 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: 1.67 (0.30), residues: 760 helix: 1.88 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.87 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 30 TYR 0.050 0.002 TYR S 80 PHE 0.009 0.002 PHE O 67 HIS 0.009 0.001 HIS O 39 Details of bonding type rmsd covalent geometry : bond 0.00420 (13403) covalent geometry : angle 0.64663 (19459) hydrogen bonds : bond 0.06517 ( 792) hydrogen bonds : angle 3.06043 ( 1932) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: I 125 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8116 (mt0) REVERT: K 25 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.7437 (t80) REVERT: M 37 TYR cc_start: 0.8600 (m-80) cc_final: 0.8208 (m-10) REVERT: M 83 ARG cc_start: 0.8081 (mtt-85) cc_final: 0.7873 (mtt90) REVERT: M 90 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: M 106 HIS cc_start: 0.8420 (OUTLIER) cc_final: 0.8153 (m170) REVERT: Q 77 LYS cc_start: 0.8095 (mmmt) cc_final: 0.7752 (mmmt) outliers start: 34 outliers final: 27 residues processed: 150 average time/residue: 0.1686 time to fit residues: 33.5092 Evaluate side-chains 159 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain I residue 125 GLN Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 106 HIS Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain Q residue 25 ASN Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 82 LYS Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 53 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 77 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** ** K 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.161329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.115442 restraints weight = 19825.944| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.60 r_work: 0.3399 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.6339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13403 Z= 0.210 Angle : 0.672 9.195 19459 Z= 0.384 Chirality : 0.039 0.197 2218 Planarity : 0.004 0.044 1377 Dihedral : 33.473 179.061 4271 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.59 % Allowed : 23.26 % Favored : 72.15 % 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: 1.48 (0.30), residues: 760 helix: 1.74 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.96 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 30 TYR 0.054 0.002 TYR S 80 PHE 0.019 0.002 PHE J 100 HIS 0.007 0.002 HIS O 39 Details of bonding type rmsd covalent geometry : bond 0.00483 (13403) covalent geometry : angle 0.67212 (19459) hydrogen bonds : bond 0.06596 ( 792) hydrogen bonds : angle 3.17262 ( 1932) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.328 Fit side-chains REVERT: I 125 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8270 (mt0) REVERT: J 51 TYR cc_start: 0.8999 (m-80) cc_final: 0.8715 (m-80) REVERT: K 25 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7573 (t80) REVERT: Q 77 LYS cc_start: 0.8111 (mmmt) cc_final: 0.7758 (mmmt) outliers start: 29 outliers final: 27 residues processed: 144 average time/residue: 0.1613 time to fit residues: 30.8298 Evaluate side-chains 151 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain I residue 125 GLN Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain Q residue 25 ASN Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 82 LYS Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 50 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 0.0970 chunk 100 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 chunk 53 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** ** K 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.159957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.113833 restraints weight = 19675.057| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.65 r_work: 0.3363 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.6528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13403 Z= 0.194 Angle : 0.656 9.411 19459 Z= 0.376 Chirality : 0.038 0.197 2218 Planarity : 0.005 0.043 1377 Dihedral : 33.408 179.185 4271 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.27 % Allowed : 23.58 % Favored : 72.15 % 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: 1.58 (0.30), residues: 760 helix: 1.84 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.97 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 32 TYR 0.052 0.002 TYR S 80 PHE 0.015 0.002 PHE J 100 HIS 0.007 0.001 HIS O 39 Details of bonding type rmsd covalent geometry : bond 0.00443 (13403) covalent geometry : angle 0.65574 (19459) hydrogen bonds : bond 0.06534 ( 792) hydrogen bonds : angle 3.09568 ( 1932) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: J 51 TYR cc_start: 0.8986 (m-80) cc_final: 0.8706 (m-80) REVERT: K 25 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7248 (t80) REVERT: M 37 TYR cc_start: 0.8610 (m-80) cc_final: 0.8210 (m-10) REVERT: Q 25 ASN cc_start: 0.7242 (OUTLIER) cc_final: 0.6795 (m-40) REVERT: Q 77 LYS cc_start: 0.8085 (mmmt) cc_final: 0.7688 (mmmt) outliers start: 27 outliers final: 25 residues processed: 141 average time/residue: 0.1646 time to fit residues: 30.7895 Evaluate side-chains 149 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain Q residue 25 ASN Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 82 LYS Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 58 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** ** K 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.158200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.111944 restraints weight = 19685.720| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.65 r_work: 0.3333 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.6680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13403 Z= 0.212 Angle : 0.671 9.410 19459 Z= 0.383 Chirality : 0.039 0.203 2218 Planarity : 0.005 0.044 1377 Dihedral : 33.485 179.253 4271 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.43 % Allowed : 23.42 % Favored : 72.15 % 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: 1.47 (0.30), residues: 760 helix: 1.76 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.02 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 32 TYR 0.055 0.002 TYR S 80 PHE 0.016 0.002 PHE J 100 HIS 0.007 0.001 HIS O 39 Details of bonding type rmsd covalent geometry : bond 0.00486 (13403) covalent geometry : angle 0.67088 (19459) hydrogen bonds : bond 0.06581 ( 792) hydrogen bonds : angle 3.15876 ( 1932) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3390.33 seconds wall clock time: 58 minutes 47.27 seconds (3527.27 seconds total)