Starting phenix.real_space_refine on Thu Aug 6 05:35:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vfy_43194/08_2026/8vfy_43194.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vfy_43194/08_2026/8vfy_43194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vfy_43194/08_2026/8vfy_43194.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vfy_43194/08_2026/8vfy_43194.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vfy_43194/08_2026/8vfy_43194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vfy_43194/08_2026/8vfy_43194.map" } resolution = 2.89 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= 0.001 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 342 5.49 5 S 21 5.16 5 C 7786 2.51 5 N 2611 2.21 5 O 3286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s 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: 14046 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" 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: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" 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: "G" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 927 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3501 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Chain: "J" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3510 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Chain: "O" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 856 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 94} Time building chain proxies: 3.18, per 1000 atoms: 0.23 Number of scatterers: 14046 At special positions: 0 Unit cell: (84.48, 118.8, 192.72, 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 21 16.00 P 342 15.00 O 3286 8.00 N 2611 7.00 C 7786 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: 1.19 Conformation dependent library (CDL) restraints added in 423.0 milliseconds 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1648 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 11 sheets defined 68.1% alpha, 3.2% beta 171 base pairs and 306 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.618A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 40 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.742A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 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: 4.370A 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 'C' and resid 112 through 116 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 103 through 123 removed outlier: 3.549A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.537A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) 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 24 through 29 removed outlier: 3.809A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.637A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.507A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.323A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.527A 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 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 removed outlier: 3.561A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL H 111 " --> pdb=" O ALA H 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 186 Processing helix chain 'O' and resid 192 through 204 Processing helix chain 'O' and resid 205 through 209 removed outlier: 3.690A pdb=" N GLN O 209 " --> pdb=" O TYR O 206 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 225 removed outlier: 4.029A pdb=" N TRP O 214 " --> pdb=" O ASN O 210 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.804A 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 96 through 98 removed outlier: 6.521A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.486A 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 101 through 102 removed outlier: 6.723A 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: 7.520A 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: 7.468A 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 Processing sheet with id=AB2, first strand: chain 'O' and resid 228 through 231 436 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 417 hydrogen bonds 834 hydrogen bond angles 0 basepair planarities 171 basepair parallelities 306 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 1.63 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: 2566 1.33 - 1.45: 4879 1.45 - 1.57: 6846 1.57 - 1.69: 682 1.69 - 1.81: 35 Bond restraints: 15008 Sorted by residual: bond pdb=" C1' DT I 29 " pdb=" N1 DT I 29 " ideal model delta sigma weight residual 1.468 1.537 -0.069 1.40e-02 5.10e+03 2.40e+01 bond pdb=" C1' DT J 67 " pdb=" N1 DT J 67 " ideal model delta sigma weight residual 1.468 1.534 -0.066 1.40e-02 5.10e+03 2.24e+01 bond pdb=" C1' DT J 55 " pdb=" N1 DT J 55 " ideal model delta sigma weight residual 1.468 1.534 -0.066 1.40e-02 5.10e+03 2.23e+01 bond pdb=" C1' DT I 102 " pdb=" N1 DT I 102 " ideal model delta sigma weight residual 1.468 1.534 -0.066 1.40e-02 5.10e+03 2.20e+01 bond pdb=" C1' DC J 56 " pdb=" N1 DC J 56 " ideal model delta sigma weight residual 1.468 1.532 -0.064 1.40e-02 5.10e+03 2.10e+01 ... (remaining 15003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 19056 1.17 - 2.33: 1887 2.33 - 3.50: 698 3.50 - 4.66: 84 4.66 - 5.83: 6 Bond angle restraints: 21731 Sorted by residual: angle pdb=" O4' DG J 28 " pdb=" C1' DG J 28 " pdb=" N9 DG J 28 " ideal model delta sigma weight residual 108.00 111.47 -3.47 7.00e-01 2.04e+00 2.46e+01 angle pdb=" N3 DT I 140 " pdb=" C4 DT I 140 " pdb=" O4 DT I 140 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.09e+01 angle pdb=" O4' DG I 131 " pdb=" C4' DG I 131 " pdb=" C3' DG I 131 " ideal model delta sigma weight residual 106.00 103.28 2.72 6.00e-01 2.78e+00 2.06e+01 angle pdb=" N3 DT I 70 " pdb=" C4 DT I 70 " pdb=" O4 DT I 70 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 angle pdb=" N3 DT J 31 " pdb=" C4 DT J 31 " pdb=" O4 DT J 31 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 ... (remaining 21726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.36: 6504 31.36 - 62.73: 1665 62.73 - 94.09: 52 94.09 - 125.46: 0 125.46 - 156.82: 2 Dihedral angle restraints: 8223 sinusoidal: 5666 harmonic: 2557 Sorted by residual: dihedral pdb=" C4' DG J 127 " pdb=" C3' DG J 127 " pdb=" O3' DG J 127 " pdb=" P DG J 128 " ideal model delta sinusoidal sigma weight residual 220.00 63.18 156.82 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" C4' DC J 93 " pdb=" C3' DC J 93 " pdb=" O3' DC J 93 " pdb=" P DC J 94 " ideal model delta sinusoidal sigma weight residual 220.00 68.58 151.42 1 3.50e+01 8.16e-04 1.47e+01 dihedral pdb=" CA LYS O 237 " pdb=" C LYS O 237 " pdb=" N PRO O 238 " pdb=" CA PRO O 238 " ideal model delta harmonic sigma weight residual 180.00 162.38 17.62 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 8220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1635 0.038 - 0.077: 406 0.077 - 0.115: 139 0.115 - 0.153: 223 0.153 - 0.192: 44 Chirality restraints: 2447 Sorted by residual: chirality pdb=" C3' DT I 121 " pdb=" C4' DT I 121 " pdb=" O3' DT I 121 " pdb=" C2' DT I 121 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" C3' DG I 122 " pdb=" C4' DG I 122 " pdb=" O3' DG I 122 " pdb=" C2' DG I 122 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" C3' DA I 152 " pdb=" C4' DA I 152 " pdb=" O3' DA I 152 " pdb=" C2' DA I 152 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.28e-01 ... (remaining 2444 not shown) Planarity restraints: 1565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS O 237 " -0.048 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO O 238 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO O 238 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO O 238 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 140 " 0.038 2.00e-02 2.50e+03 1.78e-02 7.88e+00 pdb=" N1 DT I 140 " -0.036 2.00e-02 2.50e+03 pdb=" C2 DT I 140 " -0.008 2.00e-02 2.50e+03 pdb=" O2 DT I 140 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DT I 140 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DT I 140 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT I 140 " 0.015 2.00e-02 2.50e+03 pdb=" C5 DT I 140 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT I 140 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DT I 140 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO O 171 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO O 172 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO O 172 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO O 172 " 0.027 5.00e-02 4.00e+02 ... (remaining 1562 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1294 2.74 - 3.28: 12610 3.28 - 3.82: 27731 3.82 - 4.36: 32977 4.36 - 4.90: 47101 Nonbonded interactions: 121713 Sorted by model distance: nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.203 3.040 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR B 72 " pdb=" OE2 GLU D 76 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR F 72 " pdb=" OE2 GLU H 76 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 2.275 3.040 ... (remaining 121708 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 10 through 118) } 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: 1.490 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: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.460 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 : 0.007 0.069 15008 Z= 0.606 Angle : 0.840 5.829 21731 Z= 0.748 Chirality : 0.059 0.192 2447 Planarity : 0.005 0.073 1565 Dihedral : 26.421 156.825 6575 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.74 % Favored : 98.15 % Rotamer: Outliers : 0.27 % Allowed : 1.21 % Favored : 98.52 % 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: 2.05 (0.29), residues: 863 helix: 2.21 (0.22), residues: 577 sheet: -1.65 (1.37), residues: 12 loop : -0.34 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 42 TYR 0.007 0.001 TYR G 57 PHE 0.007 0.001 PHE E 104 TRP 0.007 0.001 TRP O 214 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00715 / 0.61 (15008) covalent geometry : angle 0.84035 / 0.75 (21731) hydrogen bonds : bond 0.09755 / 6.21 ( 853) hydrogen bonds : angle 3.64263 / 2.66 ( 2112) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 184 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8872 (p) cc_final: 0.8314 (t) REVERT: A 76 GLN cc_start: 0.8172 (mt0) cc_final: 0.7705 (mt0) REVERT: B 85 ASP cc_start: 0.9142 (m-30) cc_final: 0.8911 (m-30) REVERT: C 90 ASP cc_start: 0.8325 (t0) cc_final: 0.8071 (t0) REVERT: C 95 LYS cc_start: 0.9288 (ttpt) cc_final: 0.9063 (tttm) REVERT: D 108 LYS cc_start: 0.8240 (ptmm) cc_final: 0.8016 (ptpp) REVERT: E 79 LYS cc_start: 0.8722 (ttmt) cc_final: 0.8519 (mtpm) REVERT: G 120 THR cc_start: 0.8473 (p) cc_final: 0.8053 (p) REVERT: H 59 MET cc_start: 0.9127 (tpp) cc_final: 0.8898 (tpt) REVERT: H 113 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8341 (tt0) REVERT: H 115 THR cc_start: 0.9240 (m) cc_final: 0.9029 (p) outliers start: 2 outliers final: 1 residues processed: 186 average time/residue: 0.8337 time to fit residues: 165.2076 Evaluate side-chains 119 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 30.0000 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.105432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.068984 restraints weight = 35502.110| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.04 r_work: 0.3079 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15008 Z= 0.199 Angle : 0.722 8.385 21731 Z= 0.421 Chirality : 0.048 0.344 2447 Planarity : 0.005 0.078 1565 Dihedral : 30.269 156.088 4803 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.97 % Favored : 97.91 % Rotamer: Outliers : 1.75 % Allowed : 13.23 % Favored : 85.02 % 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: 2.01 (0.28), residues: 863 helix: 2.09 (0.21), residues: 583 sheet: -1.59 (1.31), residues: 12 loop : -0.17 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 99 TYR 0.017 0.002 TYR O 197 PHE 0.017 0.002 PHE O 254 TRP 0.030 0.004 TRP O 199 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.20 (15008) covalent geometry : angle 0.72228 / 0.42 (21731) hydrogen bonds : bond 0.05288 / 3.53 ( 853) hydrogen bonds : angle 3.20715 / 2.34 ( 2112) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8825 (p) cc_final: 0.8360 (t) REVERT: A 76 GLN cc_start: 0.8362 (mt0) cc_final: 0.7955 (mt0) REVERT: C 13 LYS cc_start: 0.9113 (tppp) cc_final: 0.8831 (tppp) REVERT: C 90 ASP cc_start: 0.8272 (t0) cc_final: 0.8022 (t0) REVERT: D 63 ASN cc_start: 0.8620 (OUTLIER) cc_final: 0.8182 (m-40) REVERT: D 108 LYS cc_start: 0.8238 (ptmm) cc_final: 0.7989 (ptpp) REVERT: E 77 ASP cc_start: 0.9046 (m-30) cc_final: 0.8589 (t0) REVERT: H 59 MET cc_start: 0.9188 (tpp) cc_final: 0.8827 (tpt) REVERT: H 101 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8710 (mm) REVERT: H 113 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8438 (tt0) REVERT: O 190 MET cc_start: 0.6636 (ttp) cc_final: 0.6117 (tpp) outliers start: 13 outliers final: 6 residues processed: 125 average time/residue: 0.6995 time to fit residues: 93.6818 Evaluate side-chains 110 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain O residue 220 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 98 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS B 25 ASN C 38 ASN E 68 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.105328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.069048 restraints weight = 35981.187| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.13 r_work: 0.3101 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15008 Z= 0.182 Angle : 0.694 10.335 21731 Z= 0.405 Chirality : 0.046 0.360 2447 Planarity : 0.005 0.079 1565 Dihedral : 30.521 154.109 4803 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.97 % Favored : 97.91 % Rotamer: Outliers : 1.89 % Allowed : 14.44 % Favored : 83.67 % 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: 2.06 (0.28), residues: 863 helix: 2.07 (0.21), residues: 589 sheet: -1.32 (1.36), residues: 12 loop : -0.07 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.017 0.002 TYR H 40 PHE 0.009 0.001 PHE E 67 TRP 0.009 0.002 TRP O 199 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.18 (15008) covalent geometry : angle 0.69431 / 0.40 (21731) hydrogen bonds : bond 0.04910 / 3.27 ( 853) hydrogen bonds : angle 3.06221 / 2.24 ( 2112) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8792 (p) cc_final: 0.8311 (t) REVERT: A 76 GLN cc_start: 0.8235 (mt0) cc_final: 0.7788 (mt0) REVERT: A 80 THR cc_start: 0.9392 (OUTLIER) cc_final: 0.8978 (t) REVERT: B 24 ASP cc_start: 0.8061 (t0) cc_final: 0.7853 (t0) REVERT: B 88 TYR cc_start: 0.8713 (m-10) cc_final: 0.8291 (m-80) REVERT: C 13 LYS cc_start: 0.9133 (tppp) cc_final: 0.8841 (tppp) REVERT: C 90 ASP cc_start: 0.8295 (t0) cc_final: 0.8010 (t0) REVERT: D 63 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8106 (m-40) REVERT: D 108 LYS cc_start: 0.8181 (ptmm) cc_final: 0.7917 (ptpp) REVERT: E 77 ASP cc_start: 0.9057 (m-30) cc_final: 0.8661 (t0) REVERT: H 59 MET cc_start: 0.9158 (tpp) cc_final: 0.8794 (tpt) REVERT: H 113 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8452 (tt0) REVERT: O 190 MET cc_start: 0.6493 (ttp) cc_final: 0.6078 (tpp) REVERT: O 253 MET cc_start: 0.7101 (tpt) cc_final: 0.6893 (tpt) outliers start: 14 outliers final: 7 residues processed: 122 average time/residue: 0.7807 time to fit residues: 101.6223 Evaluate side-chains 117 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 220 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 100 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 75 optimal weight: 50.0000 chunk 108 optimal weight: 30.0000 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN D 47 GLN H 63 ASN O 212 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.104125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.067564 restraints weight = 35754.406| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.97 r_work: 0.3074 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15008 Z= 0.229 Angle : 0.734 15.044 21731 Z= 0.415 Chirality : 0.048 0.375 2447 Planarity : 0.005 0.079 1565 Dihedral : 30.849 154.640 4803 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.78 % Favored : 97.10 % Rotamer: Outliers : 3.10 % Allowed : 14.84 % Favored : 82.05 % 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: 1.87 (0.28), residues: 863 helix: 1.94 (0.21), residues: 584 sheet: -1.30 (1.37), residues: 12 loop : -0.16 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 86 TYR 0.020 0.002 TYR H 40 PHE 0.014 0.002 PHE O 254 TRP 0.006 0.001 TRP O 199 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.23 (15008) covalent geometry : angle 0.73368 / 0.41 (21731) hydrogen bonds : bond 0.05187 / 3.46 ( 853) hydrogen bonds : angle 3.14134 / 2.30 ( 2112) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8818 (p) cc_final: 0.8352 (t) REVERT: C 13 LYS cc_start: 0.9160 (tppp) cc_final: 0.8836 (tppp) REVERT: C 90 ASP cc_start: 0.8325 (t0) cc_final: 0.8089 (t0) REVERT: D 63 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8177 (m-40) REVERT: D 71 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8252 (mt-10) REVERT: D 108 LYS cc_start: 0.8172 (ptmm) cc_final: 0.7913 (ptpp) REVERT: E 63 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7609 (mmp80) REVERT: E 77 ASP cc_start: 0.8958 (m-30) cc_final: 0.8672 (t0) REVERT: F 24 ASP cc_start: 0.8393 (t0) cc_final: 0.7960 (t0) REVERT: H 59 MET cc_start: 0.9111 (tpp) cc_final: 0.8754 (tpt) REVERT: H 101 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8693 (mm) REVERT: H 113 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8465 (tt0) REVERT: O 190 MET cc_start: 0.6537 (ttp) cc_final: 0.6101 (tpp) REVERT: O 253 MET cc_start: 0.7046 (tpt) cc_final: 0.6783 (tpt) outliers start: 23 outliers final: 12 residues processed: 132 average time/residue: 0.7473 time to fit residues: 105.1986 Evaluate side-chains 123 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain O residue 220 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 40.0000 chunk 2 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 117 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN H 49 HIS ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.105621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.069414 restraints weight = 35726.437| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.14 r_work: 0.3109 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15008 Z= 0.147 Angle : 0.675 10.226 21731 Z= 0.391 Chirality : 0.046 0.375 2447 Planarity : 0.004 0.080 1565 Dihedral : 30.797 152.909 4803 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.43 % Favored : 97.45 % Rotamer: Outliers : 1.75 % Allowed : 16.60 % Favored : 81.65 % 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: 2.16 (0.28), residues: 863 helix: 2.11 (0.21), residues: 590 sheet: -1.37 (1.34), residues: 12 loop : 0.06 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.031 0.002 TYR B 88 PHE 0.019 0.001 PHE O 254 TRP 0.025 0.005 TRP O 199 HIS 0.003 0.000 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.15 (15008) covalent geometry : angle 0.67488 / 0.39 (21731) hydrogen bonds : bond 0.04464 / 2.96 ( 853) hydrogen bonds : angle 2.92836 / 2.15 ( 2112) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8744 (p) cc_final: 0.8281 (t) REVERT: B 24 ASP cc_start: 0.7728 (t0) cc_final: 0.7443 (t0) REVERT: C 90 ASP cc_start: 0.8225 (t0) cc_final: 0.8008 (t0) REVERT: D 57 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8908 (mtpt) REVERT: D 63 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8001 (m-40) REVERT: D 71 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8225 (mt-10) REVERT: D 108 LYS cc_start: 0.7986 (ptmm) cc_final: 0.7665 (ptpp) REVERT: D 113 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8619 (tp30) REVERT: E 77 ASP cc_start: 0.8954 (m-30) cc_final: 0.8680 (t0) REVERT: F 24 ASP cc_start: 0.8262 (t0) cc_final: 0.7721 (t0) REVERT: H 31 ARG cc_start: 0.8304 (pmt170) cc_final: 0.7387 (ptt-90) REVERT: H 59 MET cc_start: 0.9140 (tpp) cc_final: 0.8591 (tpt) REVERT: O 190 MET cc_start: 0.6292 (ttp) cc_final: 0.5855 (tpp) REVERT: O 253 MET cc_start: 0.6687 (tpt) cc_final: 0.6461 (tpt) outliers start: 13 outliers final: 7 residues processed: 129 average time/residue: 0.7224 time to fit residues: 99.7400 Evaluate side-chains 123 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 220 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 50 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.103158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.066561 restraints weight = 35826.810| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.12 r_work: 0.3051 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 15008 Z= 0.280 Angle : 0.758 9.635 21731 Z= 0.424 Chirality : 0.049 0.346 2447 Planarity : 0.006 0.080 1565 Dihedral : 31.089 155.026 4803 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.67 % Favored : 97.22 % Rotamer: Outliers : 2.43 % Allowed : 17.81 % Favored : 79.76 % 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: 1.65 (0.28), residues: 863 helix: 1.76 (0.21), residues: 588 sheet: -1.44 (1.33), residues: 12 loop : -0.23 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 86 TYR 0.022 0.002 TYR B 88 PHE 0.010 0.002 PHE E 67 TRP 0.012 0.002 TRP O 199 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.28 (15008) covalent geometry : angle 0.75837 / 0.42 (21731) hydrogen bonds : bond 0.05569 / 3.72 ( 853) hydrogen bonds : angle 3.23607 / 2.38 ( 2112) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8849 (p) cc_final: 0.8369 (t) REVERT: A 60 LEU cc_start: 0.8779 (mm) cc_final: 0.8562 (mt) REVERT: C 90 ASP cc_start: 0.8325 (t0) cc_final: 0.8090 (t0) REVERT: D 57 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8953 (mtpt) REVERT: D 63 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.8145 (m-40) REVERT: D 71 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8262 (mt-10) REVERT: D 108 LYS cc_start: 0.8211 (ptmm) cc_final: 0.7925 (ptpp) REVERT: E 77 ASP cc_start: 0.8994 (m-30) cc_final: 0.8722 (t0) REVERT: F 24 ASP cc_start: 0.8386 (t0) cc_final: 0.7918 (t0) REVERT: G 95 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8612 (ttpp) REVERT: G 116 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8815 (mt) REVERT: O 190 MET cc_start: 0.6465 (ttp) cc_final: 0.5992 (tpp) REVERT: O 253 MET cc_start: 0.6804 (tpt) cc_final: 0.6560 (tpt) outliers start: 18 outliers final: 8 residues processed: 122 average time/residue: 0.8282 time to fit residues: 107.5174 Evaluate side-chains 120 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 220 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 93 optimal weight: 9.9990 chunk 22 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 80 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 114 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 38 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.105629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.069102 restraints weight = 35301.803| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.26 r_work: 0.3108 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15008 Z= 0.142 Angle : 0.681 11.042 21731 Z= 0.391 Chirality : 0.045 0.338 2447 Planarity : 0.004 0.081 1565 Dihedral : 30.960 152.767 4803 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.32 % Favored : 97.57 % Rotamer: Outliers : 1.62 % Allowed : 19.97 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.28), residues: 863 helix: 2.10 (0.21), residues: 590 sheet: -1.19 (1.37), residues: 12 loop : 0.04 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.022 0.002 TYR H 40 PHE 0.011 0.001 PHE E 67 TRP 0.008 0.001 TRP O 199 HIS 0.002 0.000 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (15008) covalent geometry : angle 0.68072 / 0.39 (21731) hydrogen bonds : bond 0.04348 / 2.89 ( 853) hydrogen bonds : angle 2.94768 / 2.18 ( 2112) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8772 (p) cc_final: 0.8308 (t) REVERT: A 60 LEU cc_start: 0.8777 (mm) cc_final: 0.8556 (mt) REVERT: C 90 ASP cc_start: 0.8173 (t0) cc_final: 0.7958 (t0) REVERT: D 63 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.7970 (m-40) REVERT: D 71 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8242 (mt-10) REVERT: D 108 LYS cc_start: 0.8008 (ptmm) cc_final: 0.7697 (ptpp) REVERT: E 77 ASP cc_start: 0.8990 (m-30) cc_final: 0.8727 (t0) REVERT: F 24 ASP cc_start: 0.8364 (t0) cc_final: 0.7856 (t0) REVERT: G 95 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8561 (ttpp) REVERT: H 31 ARG cc_start: 0.8320 (pmt170) cc_final: 0.7520 (ptt-90) REVERT: O 190 MET cc_start: 0.6279 (ttp) cc_final: 0.5812 (tpp) outliers start: 12 outliers final: 4 residues processed: 124 average time/residue: 0.7513 time to fit residues: 99.4671 Evaluate side-chains 121 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 220 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 115 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 56 optimal weight: 0.5980 chunk 16 optimal weight: 0.0470 chunk 48 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 38 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.105922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.069919 restraints weight = 35753.398| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.13 r_work: 0.3101 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15008 Z= 0.141 Angle : 0.659 8.556 21731 Z= 0.384 Chirality : 0.044 0.330 2447 Planarity : 0.004 0.081 1565 Dihedral : 30.848 152.324 4803 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.20 % Favored : 97.68 % Rotamer: Outliers : 1.35 % Allowed : 20.51 % Favored : 78.14 % 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: 2.29 (0.28), residues: 863 helix: 2.21 (0.21), residues: 590 sheet: -0.90 (1.42), residues: 12 loop : 0.10 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 86 TYR 0.020 0.001 TYR B 88 PHE 0.011 0.001 PHE O 254 TRP 0.008 0.001 TRP O 199 HIS 0.002 0.000 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (15008) covalent geometry : angle 0.65856 / 0.38 (21731) hydrogen bonds : bond 0.04196 / 2.79 ( 853) hydrogen bonds : angle 2.89579 / 2.14 ( 2112) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8661 (p) cc_final: 0.8226 (t) REVERT: A 94 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8531 (mm-30) REVERT: C 50 TYR cc_start: 0.8853 (t80) cc_final: 0.8643 (t80) REVERT: D 63 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8085 (m-40) REVERT: D 71 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8275 (mt-10) REVERT: D 108 LYS cc_start: 0.8054 (ptmm) cc_final: 0.7754 (ptpp) REVERT: E 77 ASP cc_start: 0.8958 (m-30) cc_final: 0.8741 (t0) REVERT: F 24 ASP cc_start: 0.8349 (t0) cc_final: 0.7860 (t0) REVERT: H 31 ARG cc_start: 0.8294 (pmt170) cc_final: 0.7535 (ptt-90) REVERT: O 190 MET cc_start: 0.6409 (ttp) cc_final: 0.5806 (tpp) outliers start: 10 outliers final: 6 residues processed: 122 average time/residue: 0.7868 time to fit residues: 102.2714 Evaluate side-chains 124 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 220 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 87 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 112 optimal weight: 0.0470 chunk 24 optimal weight: 0.3980 chunk 109 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 116 optimal weight: 0.0170 chunk 56 optimal weight: 0.5980 chunk 110 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN G 104 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.106609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.070262 restraints weight = 35649.420| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.30 r_work: 0.3138 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15008 Z= 0.139 Angle : 0.670 11.117 21731 Z= 0.384 Chirality : 0.044 0.325 2447 Planarity : 0.004 0.081 1565 Dihedral : 30.823 152.063 4803 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.20 % Favored : 97.68 % Rotamer: Outliers : 1.75 % Allowed : 20.24 % Favored : 78.00 % 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: 2.38 (0.28), residues: 863 helix: 2.28 (0.21), residues: 590 sheet: -0.86 (1.44), residues: 12 loop : 0.12 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.024 0.001 TYR B 88 PHE 0.010 0.001 PHE O 254 TRP 0.007 0.001 TRP O 199 HIS 0.002 0.000 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (15008) covalent geometry : angle 0.66999 / 0.38 (21731) hydrogen bonds : bond 0.04097 / 2.73 ( 853) hydrogen bonds : angle 2.84711 / 2.11 ( 2112) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8585 (p) cc_final: 0.8138 (t) REVERT: C 50 TYR cc_start: 0.8932 (t80) cc_final: 0.8695 (t80) REVERT: D 63 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.8068 (m-40) REVERT: D 108 LYS cc_start: 0.8035 (ptmm) cc_final: 0.7712 (ptpp) REVERT: E 77 ASP cc_start: 0.8964 (m-30) cc_final: 0.8739 (t0) REVERT: F 24 ASP cc_start: 0.8322 (t0) cc_final: 0.7922 (t0) REVERT: H 31 ARG cc_start: 0.8264 (pmt170) cc_final: 0.7543 (ptt-90) REVERT: O 190 MET cc_start: 0.6508 (ttp) cc_final: 0.5815 (tpp) outliers start: 13 outliers final: 6 residues processed: 122 average time/residue: 0.8000 time to fit residues: 103.7795 Evaluate side-chains 121 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 220 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 43 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 13 optimal weight: 0.0270 chunk 65 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN H 63 ASN ** O 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.106989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.071070 restraints weight = 35841.180| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.02 r_work: 0.3134 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 15008 Z= 0.134 Angle : 0.653 9.182 21731 Z= 0.380 Chirality : 0.043 0.321 2447 Planarity : 0.004 0.081 1565 Dihedral : 30.772 151.890 4803 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.20 % Favored : 97.68 % Rotamer: Outliers : 0.94 % Allowed : 21.86 % Favored : 77.19 % 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: 2.36 (0.28), residues: 863 helix: 2.26 (0.21), residues: 590 sheet: -0.90 (1.45), residues: 12 loop : 0.12 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 86 TYR 0.027 0.002 TYR B 88 PHE 0.009 0.001 PHE E 67 TRP 0.007 0.001 TRP O 199 HIS 0.002 0.000 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.13 (15008) covalent geometry : angle 0.65313 / 0.38 (21731) hydrogen bonds : bond 0.04007 / 2.67 ( 853) hydrogen bonds : angle 2.83975 / 2.11 ( 2112) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8488 (p) cc_final: 0.8078 (t) REVERT: C 13 LYS cc_start: 0.9103 (tppp) cc_final: 0.8827 (tppp) REVERT: D 47 GLN cc_start: 0.8765 (tt0) cc_final: 0.8300 (tt0) REVERT: D 59 MET cc_start: 0.9074 (tpt) cc_final: 0.8468 (mmm) REVERT: D 63 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.8061 (m-40) REVERT: D 108 LYS cc_start: 0.8105 (ptmm) cc_final: 0.7790 (ptpp) REVERT: D 113 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8607 (tp30) REVERT: E 77 ASP cc_start: 0.8945 (m-30) cc_final: 0.8729 (t0) REVERT: F 24 ASP cc_start: 0.8231 (t0) cc_final: 0.7875 (t0) REVERT: H 31 ARG cc_start: 0.8246 (pmt170) cc_final: 0.7866 (ptt-90) REVERT: H 113 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7862 (tm-30) REVERT: O 190 MET cc_start: 0.6724 (ttp) cc_final: 0.6053 (tpp) REVERT: O 253 MET cc_start: 0.6966 (tpt) cc_final: 0.3015 (mtt) outliers start: 7 outliers final: 3 residues processed: 125 average time/residue: 0.8007 time to fit residues: 106.8156 Evaluate side-chains 119 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 220 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 83 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN G 89 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.107095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.071541 restraints weight = 35577.336| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.03 r_work: 0.3142 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 15008 Z= 0.136 Angle : 0.664 11.590 21731 Z= 0.379 Chirality : 0.043 0.319 2447 Planarity : 0.004 0.081 1565 Dihedral : 30.772 151.974 4803 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.97 % Favored : 97.91 % Rotamer: Outliers : 0.67 % Allowed : 22.27 % Favored : 77.06 % 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: 2.42 (0.28), residues: 863 helix: 2.31 (0.21), residues: 590 sheet: -0.81 (1.51), residues: 12 loop : 0.13 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 86 TYR 0.041 0.002 TYR B 88 PHE 0.009 0.001 PHE E 67 TRP 0.007 0.001 TRP O 199 HIS 0.002 0.000 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.14 (15008) covalent geometry : angle 0.66408 / 0.38 (21731) hydrogen bonds : bond 0.03974 / 2.65 ( 853) hydrogen bonds : angle 2.80979 / 2.08 ( 2112) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4915.33 seconds wall clock time: 84 minutes 10.44 seconds (5050.44 seconds total)