Starting phenix.real_space_refine on Fri Jul 3 10:52:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vfy_43194/07_2026/8vfy_43194.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vfy_43194/07_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_43194/07_2026/8vfy_43194.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vfy_43194/07_2026/8vfy_43194.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vfy_43194/07_2026/8vfy_43194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vfy_43194/07_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-dev-6108/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: 2.78, per 1000 atoms: 0.20 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: 1.10 Conformation dependent library (CDL) restraints added in 416.3 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: 1.86 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: 2.75 Time building geometry restraints manager: 1.52 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: 19114 1.17 - 2.33: 1834 2.33 - 3.50: 694 3.50 - 4.66: 83 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.650 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.230 ------------------------------------------------------------------------------- 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 : 0.833 5.829 21731 Z= 0.742 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 0.83339 / 0.74 (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 : 0.367 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: 0.7704 (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: 0.8520 (mtpm) REVERT: G 120 THR cc_start: 0.8473 (p) cc_final: 0.8052 (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: 0.9030 (p) outliers start: 2 outliers final: 1 residues processed: 186 average time/residue: 0.8836 time to fit residues: 175.1351 Evaluate side-chains 117 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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: 8.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.105294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.068675 restraints weight = 35522.556| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.19 r_work: 0.3095 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1273 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= 0.206 Angle : 0.714 8.168 21731 Z= 0.418 Chirality : 0.048 0.325 2447 Planarity : 0.005 0.079 1565 Dihedral : 30.389 157.241 4803 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.09 % Favored : 97.80 % Rotamer: Outliers : 2.02 % Allowed : 13.09 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.28), residues: 863 helix: 2.03 (0.21), residues: 587 sheet: -1.58 (1.31), residues: 12 loop : -0.16 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 99 TYR 0.017 0.002 TYR H 40 PHE 0.016 0.002 PHE O 254 TRP 0.029 0.004 TRP O 199 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.21 (15008) covalent geometry : angle 0.71366 / 0.42 (21731) hydrogen bonds : bond 0.05308 / 3.55 ( 853) hydrogen bonds : angle 3.21436 / 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 136 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8821 (p) cc_final: 0.8328 (t) REVERT: A 76 GLN cc_start: 0.8260 (mt0) cc_final: 0.7820 (mt0) REVERT: B 85 ASP cc_start: 0.9041 (m-30) cc_final: 0.8829 (m-30) REVERT: C 13 LYS cc_start: 0.9117 (tppp) cc_final: 0.8836 (tppp) REVERT: C 90 ASP cc_start: 0.8225 (t0) cc_final: 0.7944 (t0) REVERT: D 63 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8166 (m-40) REVERT: D 108 LYS cc_start: 0.8187 (ptmm) cc_final: 0.7919 (ptpp) REVERT: E 77 ASP cc_start: 0.9067 (m-30) cc_final: 0.8590 (t0) REVERT: H 31 ARG cc_start: 0.8437 (pmt170) cc_final: 0.7717 (ptt-90) REVERT: H 59 MET cc_start: 0.9165 (tpp) cc_final: 0.8841 (tpt) REVERT: H 101 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8651 (mm) REVERT: H 113 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8411 (tt0) REVERT: O 190 MET cc_start: 0.6498 (ttp) cc_final: 0.5966 (tpp) outliers start: 15 outliers final: 7 residues processed: 127 average time/residue: 0.8818 time to fit residues: 119.3904 Evaluate side-chains 110 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL 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: 9.9990 chunk 79 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 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: 0.3980 chunk 4 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.105716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.069509 restraints weight = 35972.638| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.01 r_work: 0.3091 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15008 Z= 0.164 Angle : 0.665 8.041 21731 Z= 0.395 Chirality : 0.045 0.341 2447 Planarity : 0.005 0.079 1565 Dihedral : 30.609 154.894 4803 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.85 % Favored : 98.03 % Rotamer: Outliers : 2.43 % Allowed : 14.17 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.15 (0.28), residues: 863 helix: 2.13 (0.21), residues: 589 sheet: -1.31 (1.36), residues: 12 loop : -0.02 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.019 0.002 TYR H 40 PHE 0.010 0.001 PHE E 67 TRP 0.009 0.002 TRP O 199 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (15008) covalent geometry : angle 0.66538 / 0.40 (21731) hydrogen bonds : bond 0.04776 / 3.18 ( 853) hydrogen bonds : angle 3.00162 / 2.19 ( 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 139 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8766 (p) cc_final: 0.8310 (t) REVERT: B 84 MET cc_start: 0.9031 (mmm) cc_final: 0.8723 (mmp) REVERT: B 88 TYR cc_start: 0.8735 (m-10) cc_final: 0.8435 (m-80) REVERT: C 13 LYS cc_start: 0.9129 (tppp) cc_final: 0.8850 (tppp) REVERT: C 90 ASP cc_start: 0.8325 (t0) cc_final: 0.8078 (t0) REVERT: D 63 ASN cc_start: 0.8568 (OUTLIER) cc_final: 0.8119 (m-40) REVERT: D 71 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8263 (mt-10) REVERT: D 108 LYS cc_start: 0.8162 (ptmm) cc_final: 0.7903 (ptpp) REVERT: E 77 ASP cc_start: 0.9023 (m-30) cc_final: 0.8662 (t0) REVERT: G 119 LYS cc_start: 0.8471 (mptt) cc_final: 0.8228 (mmtt) REVERT: H 31 ARG cc_start: 0.8360 (pmt170) cc_final: 0.7710 (ptt-90) REVERT: H 59 MET cc_start: 0.9172 (tpp) cc_final: 0.8623 (tpt) REVERT: O 190 MET cc_start: 0.6482 (ttp) cc_final: 0.6079 (tpp) outliers start: 18 outliers final: 9 residues processed: 127 average time/residue: 0.8450 time to fit residues: 114.5764 Evaluate side-chains 117 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 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 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: 9.9990 chunk 87 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 75 optimal weight: 40.0000 chunk 108 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS C 38 ASN D 47 GLN H 63 ASN ** 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 = 0.3910 r_free = 0.3910 target = 0.103923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.067325 restraints weight = 35767.880| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.02 r_work: 0.3067 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15008 Z= 0.242 Angle : 0.721 13.665 21731 Z= 0.412 Chirality : 0.048 0.351 2447 Planarity : 0.005 0.079 1565 Dihedral : 30.953 155.905 4803 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.90 % Favored : 96.99 % Rotamer: Outliers : 2.70 % Allowed : 15.52 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.85 (0.28), residues: 863 helix: 1.95 (0.21), residues: 584 sheet: -1.48 (1.31), residues: 12 loop : -0.22 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 86 TYR 0.019 0.002 TYR H 40 PHE 0.009 0.002 PHE E 67 TRP 0.005 0.001 TRP O 244 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.24 (15008) covalent geometry : angle 0.72138 / 0.41 (21731) hydrogen bonds : bond 0.05319 / 3.55 ( 853) hydrogen bonds : angle 3.16219 / 2.32 ( 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 137 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8822 (p) cc_final: 0.8338 (t) REVERT: C 13 LYS cc_start: 0.9160 (tppp) cc_final: 0.8836 (tppp) REVERT: C 90 ASP cc_start: 0.8318 (t0) cc_final: 0.8076 (t0) REVERT: D 63 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8191 (m-40) REVERT: D 108 LYS cc_start: 0.8178 (ptmm) cc_final: 0.7914 (ptpp) REVERT: E 63 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7660 (mmp80) REVERT: E 77 ASP cc_start: 0.8957 (m-30) cc_final: 0.8669 (t0) REVERT: F 24 ASP cc_start: 0.8305 (t0) cc_final: 0.7937 (t0) REVERT: G 116 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8882 (mp) REVERT: H 31 ARG cc_start: 0.8415 (pmt170) cc_final: 0.8187 (pmt170) REVERT: H 59 MET cc_start: 0.9112 (tpp) cc_final: 0.8752 (tpt) REVERT: H 76 GLU cc_start: 0.9151 (tp30) cc_final: 0.8922 (mm-30) REVERT: O 190 MET cc_start: 0.6526 (ttp) cc_final: 0.5985 (tpp) outliers start: 20 outliers final: 10 residues processed: 129 average time/residue: 0.8483 time to fit residues: 116.4517 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 : 0.274 ------------------------------------------------------------------------------- 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 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 120 LYS Chi-restraints excluded: chain E residue 63 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 40.0000 chunk 2 optimal weight: 0.9980 chunk 72 optimal weight: 0.3980 chunk 85 optimal weight: 9.9990 chunk 6 optimal weight: 0.5980 chunk 89 optimal weight: 9.9990 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 117 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 38 ASN H 49 HIS ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 212 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.105620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.069269 restraints weight = 35820.685| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.10 r_work: 0.3089 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15008 Z= 0.144 Angle : 0.661 9.122 21731 Z= 0.387 Chirality : 0.045 0.356 2447 Planarity : 0.004 0.080 1565 Dihedral : 30.890 154.154 4803 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.20 % Favored : 97.68 % Rotamer: Outliers : 2.29 % Allowed : 16.46 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.28), residues: 863 helix: 2.16 (0.21), residues: 590 sheet: -1.43 (1.31), residues: 12 loop : -0.02 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.020 0.001 TYR H 40 PHE 0.014 0.001 PHE O 254 TRP 0.028 0.003 TRP O 199 HIS 0.002 0.000 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (15008) covalent geometry : angle 0.66148 / 0.39 (21731) hydrogen bonds : bond 0.04453 / 2.96 ( 853) hydrogen bonds : angle 2.92704 / 2.16 ( 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 137 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8745 (p) cc_final: 0.8312 (t) REVERT: A 94 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8503 (mm-30) REVERT: C 90 ASP cc_start: 0.8284 (t0) cc_final: 0.8079 (t0) REVERT: D 57 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8950 (mtpt) REVERT: D 63 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.8021 (m-40) REVERT: D 71 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8235 (mt-10) REVERT: D 108 LYS cc_start: 0.8058 (ptmm) cc_final: 0.7750 (ptpp) REVERT: D 113 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8597 (tp30) REVERT: E 77 ASP cc_start: 0.8909 (m-30) cc_final: 0.8675 (t0) REVERT: F 24 ASP cc_start: 0.8203 (t0) cc_final: 0.7684 (t0) REVERT: H 59 MET cc_start: 0.9166 (tpp) cc_final: 0.8576 (tpt) REVERT: O 190 MET cc_start: 0.6349 (ttp) cc_final: 0.5930 (tpp) outliers start: 17 outliers final: 6 residues processed: 126 average time/residue: 0.8563 time to fit residues: 115.2004 Evaluate side-chains 121 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 94 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 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: 0.9980 chunk 46 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.105316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.069017 restraints weight = 35768.865| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.09 r_work: 0.3105 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15008 Z= 0.166 Angle : 0.662 8.011 21731 Z= 0.387 Chirality : 0.045 0.326 2447 Planarity : 0.005 0.081 1565 Dihedral : 30.913 154.164 4803 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.43 % Favored : 97.45 % 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: 2.17 (0.28), residues: 863 helix: 2.14 (0.21), residues: 590 sheet: -1.41 (1.30), residues: 12 loop : -0.00 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.017 0.002 TYR B 88 PHE 0.009 0.001 PHE E 67 TRP 0.016 0.002 TRP O 199 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.17 (15008) covalent geometry : angle 0.66241 / 0.39 (21731) hydrogen bonds : bond 0.04481 / 2.98 ( 853) hydrogen bonds : angle 2.92633 / 2.15 ( 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 137 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8737 (p) cc_final: 0.8269 (t) REVERT: A 60 LEU cc_start: 0.8698 (mm) cc_final: 0.8495 (mt) REVERT: B 24 ASP cc_start: 0.7462 (t0) cc_final: 0.7128 (t0) REVERT: C 90 ASP cc_start: 0.8222 (t0) cc_final: 0.7996 (t0) REVERT: D 57 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8917 (mtpt) REVERT: D 63 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8084 (m-40) REVERT: D 71 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8232 (mt-10) REVERT: D 108 LYS cc_start: 0.8140 (ptmm) cc_final: 0.7863 (ptpp) REVERT: E 77 ASP cc_start: 0.8964 (m-30) cc_final: 0.8728 (t0) REVERT: F 24 ASP cc_start: 0.8297 (t0) cc_final: 0.7742 (t0) REVERT: H 31 ARG cc_start: 0.8389 (pmt170) cc_final: 0.7628 (ptp90) REVERT: O 190 MET cc_start: 0.6373 (ttp) cc_final: 0.5891 (tpp) outliers start: 18 outliers final: 10 residues processed: 127 average time/residue: 0.8046 time to fit residues: 108.9735 Evaluate side-chains 125 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 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 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=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: 9.9990 chunk 70 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.103989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.067634 restraints weight = 35447.481| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.19 r_work: 0.3068 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15008 Z= 0.220 Angle : 0.703 8.505 21731 Z= 0.402 Chirality : 0.046 0.316 2447 Planarity : 0.005 0.081 1565 Dihedral : 31.128 155.066 4803 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.43 % Favored : 97.45 % Rotamer: Outliers : 2.02 % Allowed : 19.57 % 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: 1.88 (0.28), residues: 863 helix: 1.95 (0.21), residues: 588 sheet: -1.32 (1.29), residues: 12 loop : -0.20 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 86 TYR 0.020 0.002 TYR H 40 PHE 0.009 0.002 PHE O 254 TRP 0.010 0.002 TRP O 199 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.22 (15008) covalent geometry : angle 0.70256 / 0.40 (21731) hydrogen bonds : bond 0.04894 / 3.26 ( 853) hydrogen bonds : angle 3.10218 / 2.28 ( 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 133 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8824 (p) cc_final: 0.8332 (t) REVERT: A 60 LEU cc_start: 0.8751 (mm) cc_final: 0.8495 (mt) REVERT: B 24 ASP cc_start: 0.7970 (t0) cc_final: 0.7721 (t0) REVERT: C 90 ASP cc_start: 0.8258 (t0) cc_final: 0.8042 (t0) REVERT: D 63 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8099 (m-40) REVERT: D 71 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8269 (mt-10) REVERT: D 108 LYS cc_start: 0.8176 (ptmm) cc_final: 0.7891 (ptpp) REVERT: E 77 ASP cc_start: 0.8993 (m-30) cc_final: 0.8717 (t0) REVERT: F 24 ASP cc_start: 0.8386 (t0) cc_final: 0.7871 (t0) REVERT: G 95 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8582 (ttpp) REVERT: H 113 GLU cc_start: 0.8531 (tt0) cc_final: 0.8105 (tm-30) REVERT: O 190 MET cc_start: 0.6436 (ttp) cc_final: 0.6010 (tpp) outliers start: 15 outliers final: 10 residues processed: 124 average time/residue: 0.8882 time to fit residues: 117.3731 Evaluate side-chains 127 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 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 C residue 95 LYS 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 G residue 95 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 115 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 56 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN D 47 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 = 0.3914 r_free = 0.3914 target = 0.105707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.069198 restraints weight = 35585.052| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.31 r_work: 0.3111 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2128 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= 0.147 Angle : 0.665 9.343 21731 Z= 0.386 Chirality : 0.044 0.312 2447 Planarity : 0.004 0.081 1565 Dihedral : 31.053 154.024 4803 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.32 % Favored : 97.57 % Rotamer: Outliers : 1.89 % Allowed : 19.97 % 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: 2.14 (0.28), residues: 863 helix: 2.13 (0.21), residues: 590 sheet: -1.16 (1.32), 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 0.022 0.002 TYR H 40 PHE 0.011 0.001 PHE O 254 TRP 0.006 0.001 TRP O 199 HIS 0.002 0.000 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.15 (15008) covalent geometry : angle 0.66535 / 0.39 (21731) hydrogen bonds : bond 0.04297 / 2.85 ( 853) hydrogen bonds : angle 2.94434 / 2.18 ( 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 133 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8726 (p) cc_final: 0.8253 (t) REVERT: B 24 ASP cc_start: 0.7821 (t0) cc_final: 0.7494 (t0) REVERT: C 90 ASP cc_start: 0.8194 (t0) cc_final: 0.7972 (t0) REVERT: D 63 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8034 (m-40) REVERT: D 71 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8283 (mt-10) REVERT: D 108 LYS cc_start: 0.8029 (ptmm) cc_final: 0.7719 (ptpp) REVERT: E 77 ASP cc_start: 0.8982 (m-30) cc_final: 0.8714 (t0) REVERT: F 24 ASP cc_start: 0.8365 (t0) cc_final: 0.7877 (t0) REVERT: H 31 ARG cc_start: 0.8400 (pmt170) cc_final: 0.7730 (ptt90) REVERT: H 40 TYR cc_start: 0.8689 (m-80) cc_final: 0.8350 (m-80) REVERT: H 113 GLU cc_start: 0.8528 (tt0) cc_final: 0.8073 (tm-30) REVERT: O 190 MET cc_start: 0.6287 (ttp) cc_final: 0.5876 (tpp) outliers start: 14 outliers final: 8 residues processed: 123 average time/residue: 0.8571 time to fit residues: 112.5508 Evaluate side-chains 126 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR 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 63 ASN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 120 LYS 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: 0.7980 chunk 24 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 116 optimal weight: 20.0000 chunk 56 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.105240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.069067 restraints weight = 35824.337| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.13 r_work: 0.3107 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15008 Z= 0.164 Angle : 0.676 12.640 21731 Z= 0.387 Chirality : 0.044 0.307 2447 Planarity : 0.005 0.081 1565 Dihedral : 31.045 154.001 4803 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.43 % Favored : 97.45 % 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: 2.15 (0.28), residues: 863 helix: 2.13 (0.21), residues: 590 sheet: -1.21 (1.34), residues: 12 loop : -0.04 (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 0.005 0.001 TRP O 199 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 (15008) covalent geometry : angle 0.67625 / 0.39 (21731) hydrogen bonds : bond 0.04354 / 2.90 ( 853) hydrogen bonds : angle 2.94033 / 2.17 ( 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 131 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8694 (p) cc_final: 0.8243 (t) REVERT: B 24 ASP cc_start: 0.7935 (t0) cc_final: 0.7672 (t0) REVERT: D 63 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8101 (m-40) REVERT: D 71 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8298 (mt-10) REVERT: D 108 LYS cc_start: 0.8024 (ptmm) cc_final: 0.7706 (ptpp) REVERT: E 77 ASP cc_start: 0.8984 (m-30) cc_final: 0.8717 (t0) REVERT: F 24 ASP cc_start: 0.8381 (t0) cc_final: 0.7982 (t0) REVERT: H 113 GLU cc_start: 0.8529 (tt0) cc_final: 0.8070 (tm-30) REVERT: O 190 MET cc_start: 0.6405 (ttp) cc_final: 0.5988 (tpp) outliers start: 12 outliers final: 7 residues processed: 123 average time/residue: 0.7870 time to fit residues: 103.1459 Evaluate side-chains 123 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 63 ASN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 120 LYS 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: 0.9980 chunk 96 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.106144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.069859 restraints weight = 35548.485| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.30 r_work: 0.3124 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15008 Z= 0.148 Angle : 0.663 11.337 21731 Z= 0.383 Chirality : 0.043 0.303 2447 Planarity : 0.004 0.081 1565 Dihedral : 31.000 153.641 4803 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.20 % Favored : 97.68 % Rotamer: Outliers : 1.21 % Allowed : 20.92 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.28), residues: 863 helix: 2.18 (0.21), residues: 590 sheet: -1.24 (1.34), residues: 12 loop : 0.04 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 86 TYR 0.029 0.002 TYR B 88 PHE 0.009 0.001 PHE E 67 TRP 0.006 0.001 TRP O 199 HIS 0.002 0.000 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 (15008) covalent geometry : angle 0.66252 / 0.38 (21731) hydrogen bonds : bond 0.04148 / 2.75 ( 853) hydrogen bonds : angle 2.88180 / 2.14 ( 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 127 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8626 (p) cc_final: 0.8170 (t) REVERT: B 24 ASP cc_start: 0.7888 (t0) cc_final: 0.7659 (t0) REVERT: D 63 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.8070 (m-40) REVERT: D 108 LYS cc_start: 0.8017 (ptmm) cc_final: 0.7699 (ptpp) REVERT: E 77 ASP cc_start: 0.8977 (m-30) cc_final: 0.8717 (t0) REVERT: F 24 ASP cc_start: 0.8280 (t0) cc_final: 0.7923 (OUTLIER) REVERT: H 113 GLU cc_start: 0.8495 (tt0) cc_final: 0.8043 (tm-30) REVERT: O 190 MET cc_start: 0.6338 (ttp) cc_final: 0.5998 (tpp) REVERT: O 253 MET cc_start: 0.6088 (tpt) cc_final: 0.1640 (mtt) outliers start: 9 outliers final: 7 residues processed: 122 average time/residue: 0.8178 time to fit residues: 106.5265 Evaluate side-chains 120 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 63 ASN Chi-restraints excluded: chain D residue 120 LYS 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: 0.6980 chunk 69 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.106381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.070438 restraints weight = 35631.878| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.12 r_work: 0.3119 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15008 Z= 0.141 Angle : 0.659 12.214 21731 Z= 0.380 Chirality : 0.043 0.301 2447 Planarity : 0.004 0.081 1565 Dihedral : 30.949 153.576 4803 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.97 % Favored : 97.91 % Rotamer: Outliers : 1.08 % Allowed : 21.46 % Favored : 77.46 % 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: 2.30 (0.28), residues: 863 helix: 2.23 (0.21), residues: 590 sheet: -1.14 (1.38), residues: 12 loop : 0.06 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 86 TYR 0.036 0.002 TYR B 88 PHE 0.009 0.001 PHE E 67 TRP 0.005 0.001 TRP O 199 HIS 0.002 0.000 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (15008) covalent geometry : angle 0.65903 / 0.38 (21731) hydrogen bonds : bond 0.04092 / 2.72 ( 853) hydrogen bonds : angle 2.86585 / 2.13 ( 2112) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5090.85 seconds wall clock time: 87 minutes 20.83 seconds (5240.83 seconds total)