Starting phenix.real_space_refine on Wed Aug 5 21:22:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qzm_18778/08_2026/8qzm_18778.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qzm_18778/08_2026/8qzm_18778.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 { model { file = "/net/cci-nas-00/data/ceres_data/8qzm_18778/08_2026/8qzm_18778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qzm_18778/08_2026/8qzm_18778.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qzm_18778/08_2026/8qzm_18778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qzm_18778/08_2026/8qzm_18778.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.024 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 290 5.49 5 S 11 5.16 5 C 6718 2.51 5 N 2292 2.21 5 O 2830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12141 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 833 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2988 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2957 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 189 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 2.48, per 1000 atoms: 0.20 Number of scatterers: 12141 At special positions: 0 Unit cell: (77.926, 121.863, 117.718, 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 11 16.00 P 290 15.00 O 2830 8.00 N 2292 7.00 C 6718 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: 0.88 Conformation dependent library (CDL) restraints added in 362.0 milliseconds 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1462 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 69.7% alpha, 2.8% beta 137 base pairs and 256 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.680A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.610A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.554A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.560A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.842A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.586A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.787A pdb=" N ILE H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.671A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.969A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.499A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.643A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.216A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.396A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 406 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 355 hydrogen bonds 710 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 256 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 1.21 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: 2357 1.33 - 1.45: 4234 1.45 - 1.57: 5753 1.57 - 1.69: 578 1.69 - 1.81: 22 Bond restraints: 12944 Sorted by residual: bond pdb=" C3' DA J -67 " pdb=" C2' DA J -67 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DT J 64 " pdb=" C2' DT J 64 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DA J -22 " pdb=" C2' DA J -22 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.65e+00 bond pdb=" C3' DC J 7 " pdb=" C2' DC J 7 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.53e+00 bond pdb=" C3' DA I -30 " pdb=" C2' DA I -30 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.27e+00 ... (remaining 12939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 17964 1.93 - 3.85: 722 3.85 - 5.78: 15 5.78 - 7.71: 14 7.71 - 9.64: 2 Bond angle restraints: 18717 Sorted by residual: angle pdb=" O4' DC I -26 " pdb=" C4' DC I -26 " pdb=" C3' DC I -26 " ideal model delta sigma weight residual 106.00 102.64 3.36 6.00e-01 2.78e+00 3.14e+01 angle pdb=" O4' DA I 47 " pdb=" C4' DA I 47 " pdb=" C3' DA I 47 " ideal model delta sigma weight residual 106.00 103.18 2.82 6.00e-01 2.78e+00 2.21e+01 angle pdb=" N3 DT I -24 " pdb=" C4 DT I -24 " pdb=" O4 DT I -24 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" N3 DT I 9 " pdb=" C4 DT I 9 " pdb=" O4 DT I 9 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT J -43 " pdb=" C4 DT J -43 " pdb=" O4 DT J -43 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.91e+01 ... (remaining 18712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.29: 5477 32.29 - 64.58: 1525 64.58 - 96.87: 40 96.87 - 129.16: 0 129.16 - 161.45: 3 Dihedral angle restraints: 7045 sinusoidal: 4780 harmonic: 2265 Sorted by residual: dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual 220.00 58.55 161.45 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 66.42 153.58 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" C4' DC I 52 " pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sinusoidal sigma weight residual 220.00 69.26 150.74 1 3.50e+01 8.16e-04 1.47e+01 ... (remaining 7042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 2100 0.122 - 0.243: 21 0.243 - 0.365: 1 0.365 - 0.487: 0 0.487 - 0.608: 6 Chirality restraints: 2128 Sorted by residual: chirality pdb=" P DC I -58 " pdb=" OP1 DC I -58 " pdb=" OP2 DC I -58 " pdb=" O5' DC I -58 " both_signs ideal model delta sigma weight residual True 2.34 -2.94 -0.61 2.00e-01 2.50e+01 9.25e+00 chirality pdb=" P DG I 21 " pdb=" OP1 DG I 21 " pdb=" OP2 DG I 21 " pdb=" O5' DG I 21 " both_signs ideal model delta sigma weight residual True 2.34 -2.92 -0.59 2.00e-01 2.50e+01 8.64e+00 chirality pdb=" P DC I 53 " pdb=" OP1 DC I 53 " pdb=" OP2 DC I 53 " pdb=" O5' DC I 53 " both_signs ideal model delta sigma weight residual True 2.34 -2.89 -0.56 2.00e-01 2.50e+01 7.81e+00 ... (remaining 2125 not shown) Planarity restraints: 1366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.56e+00 pdb=" N PRO H 103 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -55 " -0.023 2.00e-02 2.50e+03 9.99e-03 2.74e+00 pdb=" N9 DA I -55 " 0.020 2.00e-02 2.50e+03 pdb=" C8 DA I -55 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DA I -55 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA I -55 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I -55 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I -55 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DA I -55 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I -55 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA I -55 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I -55 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 57 " 0.023 2.00e-02 2.50e+03 9.44e-03 2.67e+00 pdb=" N9 DG I 57 " -0.020 2.00e-02 2.50e+03 pdb=" C8 DG I 57 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DG I 57 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 57 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 57 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 57 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 57 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 57 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 57 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 57 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 57 " -0.001 2.00e-02 2.50e+03 ... (remaining 1363 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2319 2.79 - 3.31: 10898 3.31 - 3.84: 23587 3.84 - 4.37: 28097 4.37 - 4.90: 40245 Nonbonded interactions: 105146 Sorted by model distance: nonbonded pdb=" OE2 GLU G 61 " pdb=" NH1 ARG K 181 " model vdw 2.257 3.120 nonbonded pdb=" NE2 GLN E 125 " pdb=" OE2 GLU F 53 " model vdw 2.265 3.120 nonbonded pdb=" OG1 THR F 30 " pdb=" OP2 DC J -12 " model vdw 2.306 3.040 nonbonded pdb=" O LEU A 92 " pdb=" OG SER A 96 " model vdw 2.314 3.040 nonbonded pdb=" NH2 ARG F 35 " pdb=" OP2 DG I 8 " model vdw 2.315 3.120 ... (remaining 105141 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 'A' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 101)) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 10 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 3.440 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.600 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 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 0.040 12944 Z= 0.525 Angle : 0.762 9.637 18717 Z= 0.652 Chirality : 0.056 0.608 2128 Planarity : 0.004 0.047 1366 Dihedral : 28.215 161.446 5583 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.31 % Allowed : 11.04 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.30), residues: 763 helix: 1.82 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -0.22 (0.37), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 67 TYR 0.015 0.001 TYR A 41 PHE 0.008 0.001 PHE H 70 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.53 (12944) covalent geometry : angle 0.76249 / 0.65 (18717) hydrogen bonds : bond 0.10831 / 7.75 ( 761) hydrogen bonds : angle 4.01260 / 3.02 ( 1913) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 136 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 108 LYS cc_start: 0.8726 (ttpt) cc_final: 0.8392 (ttmt) outliers start: 2 outliers final: 1 residues processed: 136 average time/residue: 0.1722 time to fit residues: 30.0615 Evaluate side-chains 118 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 90 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 75 HIS G 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.057299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.043244 restraints weight = 45954.346| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.76 r_work: 0.2725 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12944 Z= 0.159 Angle : 0.629 8.330 18717 Z= 0.370 Chirality : 0.044 0.259 2128 Planarity : 0.004 0.041 1366 Dihedral : 30.818 168.778 4044 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.40 % Allowed : 11.66 % Favored : 86.94 % 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 are not related in a simple way. whole: 2.16 (0.30), residues: 763 helix: 2.07 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -0.28 (0.38), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 23 TYR 0.011 0.001 TYR H 40 PHE 0.009 0.001 PHE A 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.16 (12944) covalent geometry : angle 0.62872 / 0.37 (18717) hydrogen bonds : bond 0.05051 / 3.55 ( 761) hydrogen bonds : angle 3.18096 / 2.42 ( 1913) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9040 (m-30) cc_final: 0.8755 (t0) REVERT: A 105 GLU cc_start: 0.7879 (tp30) cc_final: 0.7555 (tp30) REVERT: C 41 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8237 (tm-30) REVERT: E 49 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8501 (ptp-170) REVERT: F 53 GLU cc_start: 0.8392 (tp30) cc_final: 0.8160 (tp30) REVERT: F 68 ASP cc_start: 0.9046 (m-30) cc_final: 0.8834 (m-30) outliers start: 9 outliers final: 5 residues processed: 135 average time/residue: 0.1419 time to fit residues: 24.9056 Evaluate side-chains 128 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 119 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 41 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 44 optimal weight: 0.1980 chunk 35 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.057812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.043802 restraints weight = 46646.806| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.79 r_work: 0.2755 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12944 Z= 0.137 Angle : 0.579 6.878 18717 Z= 0.350 Chirality : 0.042 0.282 2128 Planarity : 0.004 0.043 1366 Dihedral : 30.647 164.643 4041 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.87 % Allowed : 11.66 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.49 (0.30), residues: 763 helix: 2.32 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -0.16 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 99 TYR 0.012 0.001 TYR H 40 PHE 0.008 0.001 PHE A 67 HIS 0.002 0.000 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.14 (12944) covalent geometry : angle 0.57896 / 0.35 (18717) hydrogen bonds : bond 0.04256 / 2.97 ( 761) hydrogen bonds : angle 2.85604 / 2.16 ( 1913) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9012 (m-30) cc_final: 0.8720 (t0) REVERT: A 105 GLU cc_start: 0.7787 (tp30) cc_final: 0.7533 (tp30) REVERT: C 41 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8199 (tm-30) REVERT: D 68 ASP cc_start: 0.9236 (t0) cc_final: 0.8980 (t0) REVERT: D 76 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8911 (tp30) REVERT: E 49 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8477 (ptp-170) REVERT: F 68 ASP cc_start: 0.9024 (m-30) cc_final: 0.8821 (m-30) outliers start: 12 outliers final: 8 residues processed: 152 average time/residue: 0.1565 time to fit residues: 31.0581 Evaluate side-chains 143 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain K residue 181 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 76 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 88 optimal weight: 10.0000 chunk 24 optimal weight: 0.1980 chunk 21 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN G 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.057631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.043491 restraints weight = 46172.899| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.75 r_work: 0.2745 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12944 Z= 0.151 Angle : 0.589 7.467 18717 Z= 0.350 Chirality : 0.042 0.269 2128 Planarity : 0.003 0.037 1366 Dihedral : 30.650 166.573 4041 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.87 % Allowed : 14.00 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.30), residues: 763 helix: 2.48 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -0.20 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 67 TYR 0.010 0.001 TYR H 83 PHE 0.010 0.001 PHE A 67 HIS 0.002 0.000 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.15 (12944) covalent geometry : angle 0.58864 / 0.35 (18717) hydrogen bonds : bond 0.04359 / 3.04 ( 761) hydrogen bonds : angle 2.83452 / 2.15 ( 1913) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8971 (m-30) cc_final: 0.8731 (t0) REVERT: B 52 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8490 (mm-30) REVERT: C 41 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8093 (tm-30) REVERT: D 76 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8629 (mm-30) REVERT: E 49 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8524 (ptp-170) outliers start: 12 outliers final: 8 residues processed: 145 average time/residue: 0.1488 time to fit residues: 28.0635 Evaluate side-chains 135 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 122 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 93 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.056297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.042216 restraints weight = 47273.799| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.80 r_work: 0.2700 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12944 Z= 0.206 Angle : 0.637 7.653 18717 Z= 0.366 Chirality : 0.043 0.277 2128 Planarity : 0.004 0.043 1366 Dihedral : 30.882 166.604 4041 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.87 % Allowed : 14.31 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.30), residues: 763 helix: 2.43 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -0.32 (0.38), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 181 TYR 0.020 0.001 TYR H 83 PHE 0.014 0.001 PHE A 67 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.21 (12944) covalent geometry : angle 0.63674 / 0.37 (18717) hydrogen bonds : bond 0.04976 / 3.47 ( 761) hydrogen bonds : angle 2.97852 / 2.27 ( 1913) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9047 (m-30) cc_final: 0.8712 (t0) REVERT: B 52 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8681 (mm-30) REVERT: C 41 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8312 (tm-30) REVERT: F 68 ASP cc_start: 0.9006 (m-30) cc_final: 0.8788 (m-30) REVERT: H 34 LYS cc_start: 0.9333 (mmmm) cc_final: 0.9022 (mmtm) REVERT: H 35 GLU cc_start: 0.8397 (mm-30) cc_final: 0.6889 (mm-30) REVERT: H 108 LYS cc_start: 0.8914 (ttmm) cc_final: 0.8629 (ttmt) outliers start: 12 outliers final: 9 residues processed: 138 average time/residue: 0.1540 time to fit residues: 27.4013 Evaluate side-chains 130 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 122 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 14 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 94 optimal weight: 10.0000 chunk 98 optimal weight: 20.0000 chunk 65 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.056902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.042829 restraints weight = 46852.405| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.81 r_work: 0.2723 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12944 Z= 0.153 Angle : 0.599 9.382 18717 Z= 0.352 Chirality : 0.042 0.274 2128 Planarity : 0.004 0.037 1366 Dihedral : 30.795 166.839 4041 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.02 % Allowed : 14.62 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.30), residues: 763 helix: 2.53 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -0.16 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 181 TYR 0.011 0.001 TYR H 40 PHE 0.009 0.001 PHE A 67 HIS 0.003 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 (12944) covalent geometry : angle 0.59898 / 0.35 (18717) hydrogen bonds : bond 0.04194 / 2.91 ( 761) hydrogen bonds : angle 2.81812 / 2.14 ( 1913) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9054 (m-30) cc_final: 0.8712 (t0) REVERT: B 52 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8636 (mm-30) REVERT: C 41 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8280 (tm-30) REVERT: F 68 ASP cc_start: 0.9026 (m-30) cc_final: 0.8802 (m-30) REVERT: H 34 LYS cc_start: 0.9347 (mmmm) cc_final: 0.9031 (mmtm) REVERT: H 108 LYS cc_start: 0.8793 (ttmm) cc_final: 0.8509 (ttmt) outliers start: 13 outliers final: 11 residues processed: 138 average time/residue: 0.1259 time to fit residues: 22.8882 Evaluate side-chains 132 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 124 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 74 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.056980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.042934 restraints weight = 47002.611| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.83 r_work: 0.2728 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12944 Z= 0.151 Angle : 0.597 9.658 18717 Z= 0.350 Chirality : 0.041 0.272 2128 Planarity : 0.004 0.045 1366 Dihedral : 30.755 166.586 4041 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.02 % Allowed : 15.24 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.30), residues: 763 helix: 2.57 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -0.10 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 99 TYR 0.010 0.001 TYR H 40 PHE 0.010 0.001 PHE A 67 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (12944) covalent geometry : angle 0.59700 / 0.35 (18717) hydrogen bonds : bond 0.04235 / 2.95 ( 761) hydrogen bonds : angle 2.77722 / 2.11 ( 1913) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.305 Fit side-chains REVERT: A 81 ASP cc_start: 0.9032 (m-30) cc_final: 0.8708 (t0) REVERT: C 41 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8260 (tm-30) REVERT: D 68 ASP cc_start: 0.9218 (t0) cc_final: 0.8992 (t0) REVERT: F 68 ASP cc_start: 0.8999 (m-30) cc_final: 0.8773 (m-30) REVERT: H 34 LYS cc_start: 0.9396 (mmmm) cc_final: 0.9068 (mmtm) REVERT: H 108 LYS cc_start: 0.8803 (ttmm) cc_final: 0.8524 (ttmt) outliers start: 13 outliers final: 11 residues processed: 142 average time/residue: 0.1355 time to fit residues: 25.5382 Evaluate side-chains 135 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 124 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 27 optimal weight: 7.9990 chunk 99 optimal weight: 0.0370 chunk 1 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 84 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.057504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.043493 restraints weight = 46675.586| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.81 r_work: 0.2747 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12944 Z= 0.136 Angle : 0.586 10.356 18717 Z= 0.347 Chirality : 0.041 0.272 2128 Planarity : 0.003 0.036 1366 Dihedral : 30.681 166.539 4041 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.71 % Allowed : 15.86 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.93 (0.30), residues: 763 helix: 2.65 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -0.00 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 99 TYR 0.012 0.001 TYR H 40 PHE 0.008 0.001 PHE A 67 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.14 (12944) covalent geometry : angle 0.58604 / 0.35 (18717) hydrogen bonds : bond 0.03942 / 2.74 ( 761) hydrogen bonds : angle 2.71242 / 2.06 ( 1913) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.277 Fit side-chains REVERT: A 81 ASP cc_start: 0.9048 (m-30) cc_final: 0.8715 (t0) REVERT: C 41 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8245 (tm-30) REVERT: D 68 ASP cc_start: 0.9217 (t0) cc_final: 0.8832 (t0) REVERT: F 68 ASP cc_start: 0.9004 (m-30) cc_final: 0.8770 (m-30) REVERT: H 34 LYS cc_start: 0.9390 (mmmm) cc_final: 0.9041 (mmtm) outliers start: 11 outliers final: 10 residues processed: 135 average time/residue: 0.1522 time to fit residues: 26.9053 Evaluate side-chains 134 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 124 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.057140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.043165 restraints weight = 46861.908| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.80 r_work: 0.2737 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12944 Z= 0.154 Angle : 0.601 9.691 18717 Z= 0.351 Chirality : 0.041 0.270 2128 Planarity : 0.004 0.038 1366 Dihedral : 30.719 166.508 4041 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.87 % Allowed : 15.09 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.92 (0.30), residues: 763 helix: 2.64 (0.22), residues: 552 sheet: None (None), residues: 0 loop : 0.00 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 181 TYR 0.009 0.001 TYR H 40 PHE 0.010 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (12944) covalent geometry : angle 0.60146 / 0.35 (18717) hydrogen bonds : bond 0.04172 / 2.91 ( 761) hydrogen bonds : angle 2.74108 / 2.08 ( 1913) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.279 Fit side-chains REVERT: A 81 ASP cc_start: 0.9030 (m-30) cc_final: 0.8708 (t0) REVERT: C 41 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8242 (tm-30) REVERT: F 68 ASP cc_start: 0.9000 (m-30) cc_final: 0.8765 (m-30) REVERT: F 84 MET cc_start: 0.9044 (tpp) cc_final: 0.8765 (mmm) REVERT: H 34 LYS cc_start: 0.9401 (mmmm) cc_final: 0.9054 (mmtm) outliers start: 12 outliers final: 12 residues processed: 133 average time/residue: 0.1633 time to fit residues: 28.3931 Evaluate side-chains 133 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 50 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 39 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.057436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.043448 restraints weight = 46198.386| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 1.78 r_work: 0.2747 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12944 Z= 0.143 Angle : 0.594 9.380 18717 Z= 0.348 Chirality : 0.041 0.271 2128 Planarity : 0.003 0.036 1366 Dihedral : 30.695 166.501 4041 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.87 % Allowed : 15.71 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.97 (0.30), residues: 763 helix: 2.67 (0.22), residues: 552 sheet: None (None), residues: 0 loop : 0.05 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 99 TYR 0.010 0.001 TYR H 40 PHE 0.009 0.001 PHE A 67 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (12944) covalent geometry : angle 0.59422 / 0.35 (18717) hydrogen bonds : bond 0.03996 / 2.78 ( 761) hydrogen bonds : angle 2.69415 / 2.04 ( 1913) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.271 Fit side-chains REVERT: A 81 ASP cc_start: 0.9027 (m-30) cc_final: 0.8711 (t0) REVERT: C 41 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8248 (tm-30) REVERT: D 68 ASP cc_start: 0.9193 (t0) cc_final: 0.8931 (t0) REVERT: F 68 ASP cc_start: 0.8985 (m-30) cc_final: 0.8753 (m-30) REVERT: F 84 MET cc_start: 0.9047 (tpp) cc_final: 0.8760 (mmm) REVERT: H 34 LYS cc_start: 0.9391 (mmmm) cc_final: 0.9054 (mmtm) outliers start: 12 outliers final: 12 residues processed: 137 average time/residue: 0.1583 time to fit residues: 28.4225 Evaluate side-chains 134 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 50 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 83 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.056728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.042685 restraints weight = 46782.294| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.81 r_work: 0.2722 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12944 Z= 0.171 Angle : 0.615 9.020 18717 Z= 0.355 Chirality : 0.042 0.270 2128 Planarity : 0.004 0.046 1366 Dihedral : 30.787 166.534 4041 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.71 % Allowed : 16.02 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.90 (0.30), residues: 763 helix: 2.61 (0.22), residues: 552 sheet: None (None), residues: 0 loop : 0.05 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 187 TYR 0.009 0.001 TYR H 40 PHE 0.011 0.001 PHE A 67 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.17 (12944) covalent geometry : angle 0.61517 / 0.36 (18717) hydrogen bonds : bond 0.04401 / 3.07 ( 761) hydrogen bonds : angle 2.77674 / 2.11 ( 1913) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2301.55 seconds wall clock time: 40 minutes 5.33 seconds (2405.33 seconds total)