Starting phenix.real_space_refine on Fri Sep 11 16:10:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dbh_30631/09_2026/7dbh_30631.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dbh_30631/09_2026/7dbh_30631.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dbh_30631/09_2026/7dbh_30631.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dbh_30631/09_2026/7dbh_30631.map" model { file = "/net/cci-nas-00/data/ceres_data/7dbh_30631/09_2026/7dbh_30631.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dbh_30631/09_2026/7dbh_30631.cif" } resolution = 3.6 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= 0.001 sd= 0.004 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 250 5.49 5 S 14 5.16 5 C 5902 2.51 5 N 1973 2.21 5 O 2492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10631 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 726 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 677 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "F" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "G" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 740 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2563 Classifications: {'DNA': 126} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 125} Chain: "J" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2597 Classifications: {'DNA': 126} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 125} Time building chain proxies: 2.74, per 1000 atoms: 0.26 Number of scatterers: 10631 At special positions: 0 Unit cell: (122.1, 75.9, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 250 15.00 O 2492 8.00 N 1973 7.00 C 5902 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 248.1 milliseconds 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1296 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 76.8% alpha, 2.9% beta 116 base pairs and 191 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.717A 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 131 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.608A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.314A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 Processing helix chain 'E' and resid 49 through 57 removed outlier: 3.638A pdb=" N SER E 57 " --> pdb=" O SER E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 47 through 76 removed outlier: 4.151A pdb=" N TYR F 51 " --> pdb=" O SER F 47 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.383A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 98 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 103 through 124 removed outlier: 3.824A pdb=" N SER H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.777A pdb=" N CYS A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.821A 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: 6.864A 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: 6.435A pdb=" N CYS 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: 7.257A 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 78 403 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 303 hydrogen bonds 594 hydrogen bond angles 0 basepair planarities 116 basepair parallelities 191 stacking parallelities Total time for adding SS restraints: 2.18 Time building geometry restraints manager: 1.36 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: 2284 1.33 - 1.45: 3447 1.45 - 1.57: 5077 1.57 - 1.69: 500 1.69 - 1.81: 22 Bond restraints: 11330 Sorted by residual: bond pdb=" C3' DA J -38 " pdb=" C2' DA J -38 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.60e+01 bond pdb=" C3' DT J 54 " pdb=" C2' DT J 54 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.51e+01 bond pdb=" C3' DG J 2 " pdb=" C2' DG J 2 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.42e+01 bond pdb=" C3' DC I 4 " pdb=" C2' DC I 4 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.42e+01 bond pdb=" C3' DC I 49 " pdb=" C2' DC I 49 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 ... (remaining 11325 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 14324 1.25 - 2.50: 1607 2.50 - 3.75: 403 3.75 - 5.00: 39 5.00 - 6.25: 12 Bond angle restraints: 16385 Sorted by residual: angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 113.71 109.21 4.50 9.50e-01 1.11e+00 2.25e+01 angle pdb=" O4' DC I 6 " pdb=" C4' DC I 6 " pdb=" C3' DC I 6 " ideal model delta sigma weight residual 106.00 103.20 2.80 6.00e-01 2.78e+00 2.18e+01 angle pdb=" O4' DT I -6 " pdb=" C1' DT I -6 " pdb=" N1 DT I -6 " ideal model delta sigma weight residual 108.00 111.14 -3.14 7.00e-01 2.04e+00 2.02e+01 angle pdb=" O4' DG J -36 " pdb=" C1' DG J -36 " pdb=" N9 DG J -36 " ideal model delta sigma weight residual 108.00 111.12 -3.12 7.00e-01 2.04e+00 1.99e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 ... (remaining 16380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.66: 4874 33.66 - 67.32: 1205 67.32 - 100.98: 41 100.98 - 134.65: 5 134.65 - 168.31: 5 Dihedral angle restraints: 6130 sinusoidal: 4116 harmonic: 2014 Sorted by residual: dihedral pdb=" C ARG A 132 " pdb=" N ARG A 132 " pdb=" CA ARG A 132 " pdb=" CB ARG A 132 " ideal model delta harmonic sigma weight residual -122.60 -133.04 10.44 0 2.50e+00 1.60e-01 1.74e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 51.69 168.31 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DC J -58 " pdb=" C3' DC J -58 " pdb=" O3' DC J -58 " pdb=" P DT J -57 " ideal model delta sinusoidal sigma weight residual 220.00 51.95 168.05 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 6127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1441 0.060 - 0.120: 224 0.120 - 0.180: 188 0.180 - 0.241: 20 0.241 - 0.301: 1 Chirality restraints: 1874 Sorted by residual: chirality pdb=" CA ARG A 132 " pdb=" N ARG A 132 " pdb=" C ARG A 132 " pdb=" CB ARG A 132 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C3' DA I -33 " pdb=" C4' DA I -33 " pdb=" O3' DA I -33 " pdb=" C2' DA I -33 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.85e-01 ... (remaining 1871 not shown) Planarity restraints: 1197 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J -36 " 0.016 2.00e-02 2.50e+03 1.08e-02 3.50e+00 pdb=" N9 DG J -36 " -0.020 2.00e-02 2.50e+03 pdb=" C8 DG J -36 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG J -36 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG J -36 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG J -36 " -0.021 2.00e-02 2.50e+03 pdb=" O6 DG J -36 " 0.015 2.00e-02 2.50e+03 pdb=" N1 DG J -36 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DG J -36 " 0.008 2.00e-02 2.50e+03 pdb=" N2 DG J -36 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG J -36 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG J -36 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 35 " -0.007 2.00e-02 2.50e+03 1.20e-02 3.22e+00 pdb=" N1 DC I 35 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DC I 35 " -0.007 2.00e-02 2.50e+03 pdb=" O2 DC I 35 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DC I 35 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DC I 35 " 0.028 2.00e-02 2.50e+03 pdb=" N4 DC I 35 " -0.017 2.00e-02 2.50e+03 pdb=" C5 DC I 35 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DC I 35 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 6 " -0.022 2.00e-02 2.50e+03 1.16e-02 3.05e+00 pdb=" N1 DC I 6 " 0.023 2.00e-02 2.50e+03 pdb=" C2 DC I 6 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DC I 6 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DC I 6 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DC I 6 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC I 6 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DC I 6 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DC I 6 " 0.003 2.00e-02 2.50e+03 ... (remaining 1194 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 1 2.14 - 2.83: 3202 2.83 - 3.52: 18486 3.52 - 4.21: 29919 4.21 - 4.90: 44435 Nonbonded interactions: 96043 Sorted by model distance: nonbonded pdb=" O ALA F 33 " pdb=" CD2 LEU F 37 " model vdw 1.451 3.460 nonbonded pdb=" O HIS H 109 " pdb=" OG SER H 112 " model vdw 2.160 3.040 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.166 3.040 nonbonded pdb=" N2 DG I 58 " pdb=" O2 DT J -57 " model vdw 2.204 3.120 nonbonded pdb=" N2 DG I -60 " pdb=" O2 DC J 61 " model vdw 2.206 3.120 ... (remaining 96038 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' and resid 55 through 132) } ncs_group { reference = (chain 'B' and resid 25 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 109) } ncs_group { reference = (chain 'D' and (resid 33 through 123 or (resid 124 and (name N or name CA or nam \ e C or name CB or name OG )))) selection = (chain 'H' and resid 33 through 124) } 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 group one per residue 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.270 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 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 : 0.008 0.045 11330 Z= 0.664 Angle : 0.886 6.252 16385 Z= 0.742 Chirality : 0.065 0.301 1874 Planarity : 0.003 0.019 1197 Dihedral : 28.574 168.307 4834 Min Nonbonded Distance : 1.451 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.17 % Allowed : 0.17 % Favored : 99.65 % Cbeta Deviations : 0.15 % 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: 0.54 (0.31), residues: 681 helix: 1.01 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.62 (0.42), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 39 TYR 0.017 0.002 TYR D 83 PHE 0.009 0.002 PHE C 25 HIS 0.011 0.002 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00806 / 0.66 (11330) covalent geometry : angle 0.88557 / 0.74 (16385) hydrogen bonds : bond 0.11044 / 7.06 ( 706) hydrogen bonds : angle 5.01185 / 3.65 ( 1782) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.208 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PRO C 109 " (corrupted residue). Skipping it. Corrupt residue: chain: C residue: PRO 109 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.9292 (mt0) cc_final: 0.9056 (mt0) REVERT: A 97 GLU cc_start: 0.8443 (tt0) cc_final: 0.8192 (tt0) REVERT: A 120 MET cc_start: 0.8495 (mtp) cc_final: 0.8029 (mtp) REVERT: A 124 THR cc_start: 0.9775 (m) cc_final: 0.9562 (p) REVERT: B 44 LYS cc_start: 0.8987 (mmmt) cc_final: 0.8685 (mmmt) REVERT: B 80 THR cc_start: 0.9530 (m) cc_final: 0.9216 (p) REVERT: B 85 ASP cc_start: 0.8843 (m-30) cc_final: 0.8590 (m-30) REVERT: C 64 GLU cc_start: 0.8535 (tp30) cc_final: 0.8137 (tp30) REVERT: C 104 GLN cc_start: 0.8689 (mp10) cc_final: 0.7988 (mp10) REVERT: D 68 ASP cc_start: 0.9159 (t70) cc_final: 0.8695 (t0) REVERT: D 71 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8782 (tm-30) REVERT: D 85 LYS cc_start: 0.9504 (mttm) cc_final: 0.9271 (mtmm) REVERT: E 80 THR cc_start: 0.8924 (p) cc_final: 0.8681 (p) REVERT: E 82 LEU cc_start: 0.9401 (mt) cc_final: 0.9021 (mt) REVERT: E 120 MET cc_start: 0.8432 (mtp) cc_final: 0.8219 (mtp) REVERT: F 50 ILE cc_start: 0.9608 (mm) cc_final: 0.9354 (mm) REVERT: F 52 GLU cc_start: 0.8730 (tp30) cc_final: 0.8450 (tm-30) REVERT: G 39 TYR cc_start: 0.9215 (m-80) cc_final: 0.8933 (m-80) REVERT: G 56 GLU cc_start: 0.9023 (tt0) cc_final: 0.8651 (tt0) REVERT: G 57 TYR cc_start: 0.8993 (t80) cc_final: 0.8687 (t80) REVERT: G 64 GLU cc_start: 0.8730 (tp30) cc_final: 0.8267 (tp30) REVERT: H 46 LYS cc_start: 0.9456 (mmmt) cc_final: 0.9216 (mmmt) REVERT: H 71 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8679 (tm-30) REVERT: H 113 GLU cc_start: 0.9257 (tp30) cc_final: 0.8775 (tt0) outliers start: 1 outliers final: 0 residues processed: 208 average time/residue: 0.1270 time to fit residues: 35.4549 Evaluate side-chains 155 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 30.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN B 93 GLN ** D 84 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 = 0.3562 r_free = 0.3562 target = 0.062676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.040133 restraints weight = 54804.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.041263 restraints weight = 29278.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.041994 restraints weight = 21313.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.042325 restraints weight = 18154.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.042571 restraints weight = 16922.823| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11330 Z= 0.174 Angle : 0.776 9.188 16385 Z= 0.445 Chirality : 0.051 0.416 1874 Planarity : 0.005 0.038 1197 Dihedral : 32.369 175.859 3499 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.73 % Allowed : 12.95 % Favored : 85.32 % 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 (0.31), residues: 681 helix: 2.17 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.10 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 132 TYR 0.044 0.002 TYR D 83 PHE 0.014 0.002 PHE A 67 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.17 (11330) covalent geometry : angle 0.77596 / 0.44 (16385) hydrogen bonds : bond 0.05523 / 3.79 ( 706) hydrogen bonds : angle 3.74081 / 2.80 ( 1782) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 209 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9786 (tp) cc_final: 0.9585 (tt) REVERT: A 85 GLN cc_start: 0.9319 (mt0) cc_final: 0.8897 (mt0) REVERT: A 94 GLU cc_start: 0.8608 (tp30) cc_final: 0.8294 (tp30) REVERT: A 97 GLU cc_start: 0.8385 (tt0) cc_final: 0.8166 (tt0) REVERT: A 124 THR cc_start: 0.9717 (m) cc_final: 0.9320 (p) REVERT: A 125 GLN cc_start: 0.9074 (mt0) cc_final: 0.8210 (mp10) REVERT: B 44 LYS cc_start: 0.8961 (mmmt) cc_final: 0.8668 (mmmt) REVERT: B 49 LEU cc_start: 0.9671 (mp) cc_final: 0.9141 (mt) REVERT: B 96 THR cc_start: 0.9491 (m) cc_final: 0.9229 (t) REVERT: C 24 GLN cc_start: 0.9359 (mm110) cc_final: 0.8885 (mp10) REVERT: C 38 ASN cc_start: 0.8427 (t0) cc_final: 0.8007 (t0) REVERT: C 64 GLU cc_start: 0.8607 (tp30) cc_final: 0.8190 (tp30) REVERT: C 104 GLN cc_start: 0.8617 (mp10) cc_final: 0.7763 (mp10) REVERT: D 68 ASP cc_start: 0.8936 (t70) cc_final: 0.8606 (t70) REVERT: D 71 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8596 (tm-30) REVERT: E 125 GLN cc_start: 0.8339 (tm-30) cc_final: 0.8116 (tm-30) REVERT: F 39 ARG cc_start: 0.9146 (tpp-160) cc_final: 0.8762 (tpp-160) REVERT: F 44 LYS cc_start: 0.9266 (mtpp) cc_final: 0.8963 (mmmm) REVERT: F 52 GLU cc_start: 0.8644 (tp30) cc_final: 0.8397 (tm-30) REVERT: F 73 THR cc_start: 0.9634 (m) cc_final: 0.9356 (p) REVERT: G 57 TYR cc_start: 0.9005 (t80) cc_final: 0.8494 (t80) REVERT: G 64 GLU cc_start: 0.8739 (tp30) cc_final: 0.8177 (tp30) REVERT: G 89 ASN cc_start: 0.9317 (m-40) cc_final: 0.9057 (m110) REVERT: H 46 LYS cc_start: 0.9382 (mmmt) cc_final: 0.9174 (mmmt) REVERT: H 71 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8553 (tm-30) REVERT: H 93 GLU cc_start: 0.8423 (mp0) cc_final: 0.8126 (mp0) REVERT: H 113 GLU cc_start: 0.9126 (tp30) cc_final: 0.8727 (tt0) outliers start: 10 outliers final: 5 residues processed: 213 average time/residue: 0.1001 time to fit residues: 30.4234 Evaluate side-chains 175 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 170 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 80 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 71 optimal weight: 30.0000 chunk 47 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 69 optimal weight: 40.0000 chunk 37 optimal weight: 0.9990 chunk 86 optimal weight: 40.0000 chunk 43 optimal weight: 4.9990 chunk 73 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 49 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** G 73 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 = 0.3545 r_free = 0.3545 target = 0.061933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.039639 restraints weight = 55645.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.040734 restraints weight = 29983.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.041449 restraints weight = 21916.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.041658 restraints weight = 18611.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.041661 restraints weight = 17386.470| |-----------------------------------------------------------------------------| r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11330 Z= 0.193 Angle : 0.729 8.961 16385 Z= 0.421 Chirality : 0.047 0.374 1874 Planarity : 0.004 0.050 1197 Dihedral : 32.321 177.477 3499 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.94 % Allowed : 17.96 % Favored : 79.10 % 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: 2.34 (0.31), residues: 681 helix: 2.26 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -0.92 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 92 TYR 0.035 0.002 TYR D 83 PHE 0.014 0.002 PHE E 78 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.19 (11330) covalent geometry : angle 0.72895 / 0.42 (16385) hydrogen bonds : bond 0.05448 / 3.70 ( 706) hydrogen bonds : angle 3.57674 / 2.66 ( 1782) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.9230 (mt0) cc_final: 0.8774 (mt0) REVERT: A 94 GLU cc_start: 0.8686 (tp30) cc_final: 0.8388 (tp30) REVERT: A 97 GLU cc_start: 0.8500 (tt0) cc_final: 0.8234 (tt0) REVERT: A 107 THR cc_start: 0.9595 (m) cc_final: 0.9394 (p) REVERT: A 125 GLN cc_start: 0.9227 (mt0) cc_final: 0.8411 (mp10) REVERT: B 44 LYS cc_start: 0.9004 (mmmt) cc_final: 0.8728 (mmmt) REVERT: B 96 THR cc_start: 0.9522 (m) cc_final: 0.9212 (p) REVERT: C 38 ASN cc_start: 0.8392 (t0) cc_final: 0.7932 (t0) REVERT: C 64 GLU cc_start: 0.8615 (tp30) cc_final: 0.8249 (tp30) REVERT: C 104 GLN cc_start: 0.8562 (mp10) cc_final: 0.8035 (mp10) REVERT: D 46 LYS cc_start: 0.9557 (mmtp) cc_final: 0.9305 (mmtp) REVERT: D 68 ASP cc_start: 0.9056 (t70) cc_final: 0.8729 (t70) REVERT: D 71 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8614 (tm-30) REVERT: D 120 LYS cc_start: 0.9540 (ttpt) cc_final: 0.9153 (ttpp) REVERT: E 125 GLN cc_start: 0.8452 (tm130) cc_final: 0.8135 (tm-30) REVERT: F 39 ARG cc_start: 0.9149 (tpp-160) cc_final: 0.8633 (tpp-160) REVERT: F 44 LYS cc_start: 0.9270 (mtpp) cc_final: 0.9010 (mmmm) REVERT: F 52 GLU cc_start: 0.8683 (tp30) cc_final: 0.8351 (tm-30) REVERT: F 63 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8352 (mt-10) REVERT: F 73 THR cc_start: 0.9644 (m) cc_final: 0.9393 (p) REVERT: G 39 TYR cc_start: 0.9263 (m-80) cc_final: 0.9007 (m-80) REVERT: G 57 TYR cc_start: 0.9044 (t80) cc_final: 0.8547 (t80) REVERT: G 64 GLU cc_start: 0.8708 (tp30) cc_final: 0.8064 (tp30) REVERT: G 89 ASN cc_start: 0.9362 (m-40) cc_final: 0.9052 (m110) REVERT: G 90 ASP cc_start: 0.8344 (t0) cc_final: 0.7977 (t0) REVERT: G 92 GLU cc_start: 0.8937 (mp0) cc_final: 0.8481 (pm20) REVERT: H 46 LYS cc_start: 0.9396 (mmmt) cc_final: 0.9174 (mmmt) REVERT: H 71 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8569 (tm-30) REVERT: H 93 GLU cc_start: 0.8575 (mp0) cc_final: 0.8307 (mp0) REVERT: H 113 GLU cc_start: 0.9164 (tp30) cc_final: 0.8742 (tt0) outliers start: 17 outliers final: 13 residues processed: 184 average time/residue: 0.1084 time to fit residues: 28.1127 Evaluate side-chains 179 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 100 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 74 optimal weight: 30.0000 chunk 67 optimal weight: 50.0000 chunk 45 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 69 optimal weight: 40.0000 chunk 16 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.062059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.039870 restraints weight = 54840.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.041035 restraints weight = 28977.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.041788 restraints weight = 20786.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.042208 restraints weight = 17484.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.042318 restraints weight = 16043.087| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11330 Z= 0.168 Angle : 0.700 8.607 16385 Z= 0.406 Chirality : 0.046 0.380 1874 Planarity : 0.004 0.039 1197 Dihedral : 32.263 178.126 3499 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.28 % Allowed : 19.34 % Favored : 77.37 % 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: 2.48 (0.32), residues: 681 helix: 2.32 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -0.78 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 92 TYR 0.041 0.002 TYR D 83 PHE 0.010 0.001 PHE E 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.17 (11330) covalent geometry : angle 0.69957 / 0.41 (16385) hydrogen bonds : bond 0.04869 / 3.31 ( 706) hydrogen bonds : angle 3.42196 / 2.53 ( 1782) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.9203 (mt0) cc_final: 0.8694 (mt0) REVERT: A 94 GLU cc_start: 0.8715 (tp30) cc_final: 0.8394 (tp30) REVERT: A 97 GLU cc_start: 0.8521 (tt0) cc_final: 0.8236 (tt0) REVERT: A 125 GLN cc_start: 0.9230 (mt0) cc_final: 0.8376 (mp10) REVERT: B 44 LYS cc_start: 0.9034 (mmmt) cc_final: 0.8742 (mmmt) REVERT: B 96 THR cc_start: 0.9527 (m) cc_final: 0.9240 (p) REVERT: C 38 ASN cc_start: 0.8396 (t0) cc_final: 0.7879 (t0) REVERT: C 64 GLU cc_start: 0.8660 (tp30) cc_final: 0.8301 (tp30) REVERT: C 73 ASN cc_start: 0.8906 (t0) cc_final: 0.8566 (t0) REVERT: C 104 GLN cc_start: 0.8558 (mp10) cc_final: 0.7939 (mp10) REVERT: D 46 LYS cc_start: 0.9507 (mmtp) cc_final: 0.9228 (mmtp) REVERT: D 68 ASP cc_start: 0.9078 (t70) cc_final: 0.8753 (t70) REVERT: D 71 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8642 (tm-30) REVERT: D 120 LYS cc_start: 0.9502 (ttpt) cc_final: 0.9156 (ttpp) REVERT: E 79 LYS cc_start: 0.8560 (tmtt) cc_final: 0.7941 (tmtt) REVERT: E 123 ASP cc_start: 0.8883 (m-30) cc_final: 0.8459 (m-30) REVERT: E 125 GLN cc_start: 0.8510 (tm130) cc_final: 0.8155 (tm-30) REVERT: F 39 ARG cc_start: 0.9201 (tpp-160) cc_final: 0.8820 (tpp-160) REVERT: F 63 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8525 (mt-10) REVERT: F 73 THR cc_start: 0.9644 (m) cc_final: 0.9397 (p) REVERT: G 39 TYR cc_start: 0.9252 (m-80) cc_final: 0.8959 (m-80) REVERT: G 64 GLU cc_start: 0.8700 (tp30) cc_final: 0.7916 (tp30) REVERT: G 68 ASN cc_start: 0.9223 (m-40) cc_final: 0.8541 (m-40) REVERT: G 84 GLN cc_start: 0.9396 (tp-100) cc_final: 0.8905 (tp-100) REVERT: G 89 ASN cc_start: 0.9354 (m-40) cc_final: 0.9023 (m110) REVERT: H 46 LYS cc_start: 0.9404 (mmmt) cc_final: 0.9148 (mmmt) REVERT: H 71 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8571 (tm-30) REVERT: H 93 GLU cc_start: 0.8503 (mp0) cc_final: 0.8121 (mp0) REVERT: H 113 GLU cc_start: 0.9156 (tp30) cc_final: 0.8703 (tt0) outliers start: 19 outliers final: 13 residues processed: 205 average time/residue: 0.1065 time to fit residues: 30.9211 Evaluate side-chains 191 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 15 optimal weight: 20.0000 chunk 73 optimal weight: 30.0000 chunk 66 optimal weight: 50.0000 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 72 optimal weight: 30.0000 chunk 86 optimal weight: 40.0000 chunk 67 optimal weight: 50.0000 chunk 85 optimal weight: 30.0000 chunk 78 optimal weight: 50.0000 chunk 36 optimal weight: 4.9990 overall best weight: 13.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 94 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN H 109 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.058560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.036185 restraints weight = 57008.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.037202 restraints weight = 31963.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.037847 restraints weight = 23761.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.038223 restraints weight = 20361.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.038326 restraints weight = 18761.964| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.066 11330 Z= 0.523 Angle : 0.957 11.237 16385 Z= 0.517 Chirality : 0.054 0.349 1874 Planarity : 0.006 0.046 1197 Dihedral : 32.537 175.733 3499 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 6.04 % Allowed : 19.17 % Favored : 74.78 % 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: 1.52 (0.30), residues: 681 helix: 1.62 (0.21), residues: 528 sheet: None (None), residues: 0 loop : -1.13 (0.46), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 42 TYR 0.059 0.004 TYR D 83 PHE 0.022 0.003 PHE E 78 HIS 0.008 0.003 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.01053 / 0.52 (11330) covalent geometry : angle 0.95712 / 0.52 (16385) hydrogen bonds : bond 0.09221 / 6.24 ( 706) hydrogen bonds : angle 4.24749 / 3.14 ( 1782) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.9015 (mmm-85) cc_final: 0.8132 (mmm-85) REVERT: A 81 ASP cc_start: 0.8451 (m-30) cc_final: 0.8146 (p0) REVERT: A 85 GLN cc_start: 0.9200 (mt0) cc_final: 0.8694 (mt0) REVERT: A 94 GLU cc_start: 0.8858 (tp30) cc_final: 0.8560 (tp30) REVERT: A 125 GLN cc_start: 0.9239 (mt0) cc_final: 0.8503 (mp10) REVERT: B 44 LYS cc_start: 0.9111 (mmmt) cc_final: 0.8881 (mmmt) REVERT: C 38 ASN cc_start: 0.8483 (t0) cc_final: 0.8120 (t0) REVERT: C 64 GLU cc_start: 0.8603 (tp30) cc_final: 0.8323 (tp30) REVERT: C 104 GLN cc_start: 0.8745 (mp10) cc_final: 0.8075 (mp10) REVERT: D 46 LYS cc_start: 0.9524 (mmtp) cc_final: 0.9299 (mmmt) REVERT: D 68 ASP cc_start: 0.9134 (t70) cc_final: 0.8552 (t0) REVERT: E 79 LYS cc_start: 0.8747 (tmtt) cc_final: 0.8110 (tmtt) REVERT: E 125 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8370 (tm-30) REVERT: F 39 ARG cc_start: 0.9229 (tpp-160) cc_final: 0.8889 (tpp-160) REVERT: F 44 LYS cc_start: 0.9273 (mtpp) cc_final: 0.9028 (mmmm) REVERT: F 53 GLU cc_start: 0.8735 (tp30) cc_final: 0.8508 (tp30) REVERT: F 63 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8606 (mt-10) REVERT: G 38 ASN cc_start: 0.9297 (m-40) cc_final: 0.9061 (m110) REVERT: G 64 GLU cc_start: 0.8621 (tp30) cc_final: 0.7807 (tp30) REVERT: G 89 ASN cc_start: 0.9384 (m-40) cc_final: 0.9052 (m110) REVERT: G 90 ASP cc_start: 0.8521 (t0) cc_final: 0.8282 (t0) REVERT: G 92 GLU cc_start: 0.9073 (mp0) cc_final: 0.8600 (pm20) REVERT: H 46 LYS cc_start: 0.9466 (mmmt) cc_final: 0.9258 (mmmt) REVERT: H 71 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8537 (tm-30) REVERT: H 93 GLU cc_start: 0.8744 (mp0) cc_final: 0.8292 (mp0) outliers start: 35 outliers final: 30 residues processed: 170 average time/residue: 0.1043 time to fit residues: 25.2943 Evaluate side-chains 174 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 70 optimal weight: 30.0000 chunk 4 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN E 85 GLN E 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.061772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.038656 restraints weight = 53871.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.039754 restraints weight = 28115.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.040457 restraints weight = 20513.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.040892 restraints weight = 17476.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.040978 restraints weight = 16070.387| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11330 Z= 0.164 Angle : 0.714 8.898 16385 Z= 0.410 Chirality : 0.048 0.379 1874 Planarity : 0.004 0.044 1197 Dihedral : 32.399 179.141 3499 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.59 % Allowed : 22.80 % Favored : 74.61 % 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: 2.39 (0.31), residues: 681 helix: 2.29 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -0.92 (0.45), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 67 TYR 0.030 0.002 TYR G 57 PHE 0.012 0.002 PHE B 61 HIS 0.006 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.16 (11330) covalent geometry : angle 0.71414 / 0.41 (16385) hydrogen bonds : bond 0.04956 / 3.30 ( 706) hydrogen bonds : angle 3.42969 / 2.55 ( 1782) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8849 (mmm-85) cc_final: 0.7972 (mmm-85) REVERT: A 85 GLN cc_start: 0.9171 (mt0) cc_final: 0.8564 (mt0) REVERT: A 94 GLU cc_start: 0.8696 (tp30) cc_final: 0.8456 (tp30) REVERT: A 125 GLN cc_start: 0.9167 (mt0) cc_final: 0.8345 (mp10) REVERT: B 96 THR cc_start: 0.9499 (m) cc_final: 0.9229 (p) REVERT: C 38 ASN cc_start: 0.8326 (t0) cc_final: 0.7855 (t0) REVERT: C 64 GLU cc_start: 0.8653 (tp30) cc_final: 0.8291 (tp30) REVERT: C 73 ASN cc_start: 0.8948 (t0) cc_final: 0.8510 (t0) REVERT: C 104 GLN cc_start: 0.8629 (mp10) cc_final: 0.7852 (mp10) REVERT: D 46 LYS cc_start: 0.9523 (mmtp) cc_final: 0.9264 (mmmt) REVERT: D 68 ASP cc_start: 0.9034 (t70) cc_final: 0.8673 (t70) REVERT: D 71 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8669 (tm-30) REVERT: D 120 LYS cc_start: 0.9553 (ttpt) cc_final: 0.9181 (ttpp) REVERT: E 79 LYS cc_start: 0.8640 (tmtt) cc_final: 0.7951 (tmtt) REVERT: E 85 GLN cc_start: 0.9102 (mt0) cc_final: 0.8864 (mt0) REVERT: E 93 GLN cc_start: 0.9166 (tp40) cc_final: 0.8772 (tp40) REVERT: E 123 ASP cc_start: 0.8807 (m-30) cc_final: 0.8433 (m-30) REVERT: E 125 GLN cc_start: 0.8533 (tm-30) cc_final: 0.8303 (tm-30) REVERT: F 39 ARG cc_start: 0.9135 (tpp-160) cc_final: 0.8764 (tpp-160) REVERT: F 63 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8476 (mt-10) REVERT: F 73 THR cc_start: 0.9680 (m) cc_final: 0.9456 (p) REVERT: G 38 ASN cc_start: 0.9129 (m-40) cc_final: 0.8633 (m110) REVERT: G 57 TYR cc_start: 0.8885 (t80) cc_final: 0.8487 (t80) REVERT: G 64 GLU cc_start: 0.8633 (tp30) cc_final: 0.7813 (tp30) REVERT: G 68 ASN cc_start: 0.9258 (m-40) cc_final: 0.8369 (m-40) REVERT: G 89 ASN cc_start: 0.9350 (m-40) cc_final: 0.8984 (m110) REVERT: G 90 ASP cc_start: 0.8519 (t0) cc_final: 0.8258 (t0) REVERT: G 92 GLU cc_start: 0.8996 (mp0) cc_final: 0.8555 (pm20) REVERT: H 46 LYS cc_start: 0.9427 (mmmt) cc_final: 0.9199 (mmmt) REVERT: H 93 GLU cc_start: 0.8611 (mp0) cc_final: 0.8180 (mp0) REVERT: H 113 GLU cc_start: 0.9225 (tp30) cc_final: 0.8864 (tt0) outliers start: 15 outliers final: 11 residues processed: 192 average time/residue: 0.1043 time to fit residues: 28.3141 Evaluate side-chains 187 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 176 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 64 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 86 optimal weight: 40.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.061448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.039278 restraints weight = 54576.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.040385 restraints weight = 29590.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.041085 restraints weight = 21629.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.041465 restraints weight = 18409.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.041567 restraints weight = 16992.647| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11330 Z= 0.170 Angle : 0.709 8.592 16385 Z= 0.405 Chirality : 0.046 0.347 1874 Planarity : 0.004 0.045 1197 Dihedral : 32.266 176.348 3499 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.42 % Allowed : 24.35 % Favored : 73.23 % 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: 2.60 (0.31), residues: 681 helix: 2.41 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -0.76 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.026 0.002 TYR G 57 PHE 0.013 0.002 PHE E 78 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.17 (11330) covalent geometry : angle 0.70853 / 0.40 (16385) hydrogen bonds : bond 0.04997 / 3.36 ( 706) hydrogen bonds : angle 3.37511 / 2.50 ( 1782) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8877 (mmm-85) cc_final: 0.7969 (mmm-85) REVERT: A 85 GLN cc_start: 0.9140 (mt0) cc_final: 0.8603 (mt0) REVERT: A 94 GLU cc_start: 0.8706 (tp30) cc_final: 0.8443 (tp30) REVERT: A 125 GLN cc_start: 0.9210 (mt0) cc_final: 0.8399 (mp10) REVERT: C 16 THR cc_start: 0.8362 (p) cc_final: 0.8109 (t) REVERT: C 20 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7080 (mtp85) REVERT: C 64 GLU cc_start: 0.8648 (tp30) cc_final: 0.8325 (tp30) REVERT: C 73 ASN cc_start: 0.8948 (t0) cc_final: 0.8515 (t0) REVERT: C 104 GLN cc_start: 0.8589 (mp10) cc_final: 0.7916 (mp10) REVERT: D 46 LYS cc_start: 0.9528 (mmtp) cc_final: 0.9242 (mmmt) REVERT: D 68 ASP cc_start: 0.9074 (t70) cc_final: 0.8788 (t70) REVERT: D 71 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8724 (tm-30) REVERT: D 120 LYS cc_start: 0.9537 (ttpt) cc_final: 0.9180 (ttpp) REVERT: E 79 LYS cc_start: 0.8630 (tmtt) cc_final: 0.7933 (tmtt) REVERT: E 123 ASP cc_start: 0.8825 (m-30) cc_final: 0.8406 (m-30) REVERT: E 125 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8349 (tm-30) REVERT: F 39 ARG cc_start: 0.9198 (tpp-160) cc_final: 0.8768 (tpp-160) REVERT: F 63 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8475 (mt-10) REVERT: F 73 THR cc_start: 0.9656 (m) cc_final: 0.9438 (p) REVERT: G 57 TYR cc_start: 0.8959 (t80) cc_final: 0.8630 (t80) REVERT: G 59 THR cc_start: 0.9705 (m) cc_final: 0.9346 (t) REVERT: G 64 GLU cc_start: 0.8583 (tp30) cc_final: 0.7761 (tp30) REVERT: G 68 ASN cc_start: 0.9259 (m-40) cc_final: 0.8286 (m-40) REVERT: G 89 ASN cc_start: 0.9375 (m-40) cc_final: 0.8990 (m110) REVERT: G 90 ASP cc_start: 0.8469 (t0) cc_final: 0.8169 (t0) REVERT: G 92 GLU cc_start: 0.9029 (mp0) cc_final: 0.8577 (pm20) REVERT: H 46 LYS cc_start: 0.9457 (mmmt) cc_final: 0.9195 (mmmt) REVERT: H 93 GLU cc_start: 0.8682 (mp0) cc_final: 0.8197 (mp0) REVERT: H 113 GLU cc_start: 0.9284 (tp30) cc_final: 0.8563 (tm-30) outliers start: 14 outliers final: 11 residues processed: 193 average time/residue: 0.0996 time to fit residues: 27.3174 Evaluate side-chains 186 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 66 optimal weight: 50.0000 chunk 80 optimal weight: 40.0000 chunk 51 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 55 GLN E 93 GLN G 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.062032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.039269 restraints weight = 53947.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.040339 restraints weight = 29354.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.041050 restraints weight = 21610.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.041469 restraints weight = 18463.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.041620 restraints weight = 17017.834| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11330 Z= 0.163 Angle : 0.700 8.325 16385 Z= 0.401 Chirality : 0.046 0.349 1874 Planarity : 0.004 0.050 1197 Dihedral : 32.174 177.270 3499 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.42 % Allowed : 24.87 % Favored : 72.71 % 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: 2.58 (0.32), residues: 681 helix: 2.38 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -0.69 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 78 TYR 0.023 0.002 TYR H 83 PHE 0.011 0.001 PHE H 70 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.16 (11330) covalent geometry : angle 0.69959 / 0.40 (16385) hydrogen bonds : bond 0.04650 / 3.13 ( 706) hydrogen bonds : angle 3.30286 / 2.44 ( 1782) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 190 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8858 (mmm-85) cc_final: 0.7946 (mmm-85) REVERT: A 85 GLN cc_start: 0.9120 (mt0) cc_final: 0.8576 (mt0) REVERT: A 94 GLU cc_start: 0.8696 (tp30) cc_final: 0.8457 (tp30) REVERT: A 125 GLN cc_start: 0.9206 (mt0) cc_final: 0.8363 (mp10) REVERT: B 84 MET cc_start: 0.8989 (tpp) cc_final: 0.8737 (mmm) REVERT: C 16 THR cc_start: 0.8383 (p) cc_final: 0.8142 (t) REVERT: C 20 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7049 (mtp85) REVERT: C 64 GLU cc_start: 0.8607 (tp30) cc_final: 0.8329 (tp30) REVERT: C 73 ASN cc_start: 0.8956 (t0) cc_final: 0.8525 (t0) REVERT: C 104 GLN cc_start: 0.8582 (mp10) cc_final: 0.7805 (mp10) REVERT: D 46 LYS cc_start: 0.9515 (mmtp) cc_final: 0.9213 (mmmt) REVERT: D 68 ASP cc_start: 0.9086 (t70) cc_final: 0.8828 (t70) REVERT: D 71 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8705 (tm-30) REVERT: D 120 LYS cc_start: 0.9542 (ttpt) cc_final: 0.9152 (ttpp) REVERT: E 63 ARG cc_start: 0.8199 (mmp-170) cc_final: 0.7947 (mmm-85) REVERT: E 79 LYS cc_start: 0.8599 (tmtt) cc_final: 0.7904 (tmtt) REVERT: E 94 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8473 (mm-30) REVERT: E 123 ASP cc_start: 0.8802 (m-30) cc_final: 0.8421 (m-30) REVERT: E 125 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8344 (tm-30) REVERT: F 39 ARG cc_start: 0.9199 (tpp-160) cc_final: 0.8620 (tpp-160) REVERT: F 63 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8489 (mt-10) REVERT: F 73 THR cc_start: 0.9667 (m) cc_final: 0.9461 (p) REVERT: G 57 TYR cc_start: 0.8935 (t80) cc_final: 0.8634 (t80) REVERT: G 59 THR cc_start: 0.9697 (m) cc_final: 0.9345 (t) REVERT: G 64 GLU cc_start: 0.8535 (tp30) cc_final: 0.7686 (tp30) REVERT: G 68 ASN cc_start: 0.9255 (m-40) cc_final: 0.8241 (m-40) REVERT: G 84 GLN cc_start: 0.9388 (tp-100) cc_final: 0.9117 (tp-100) REVERT: G 89 ASN cc_start: 0.9386 (m-40) cc_final: 0.9004 (m110) REVERT: G 90 ASP cc_start: 0.8451 (t0) cc_final: 0.8135 (t0) REVERT: G 92 GLU cc_start: 0.9023 (mp0) cc_final: 0.8564 (pm20) REVERT: H 46 LYS cc_start: 0.9448 (mmmt) cc_final: 0.9203 (mmmt) REVERT: H 59 MET cc_start: 0.9338 (tpp) cc_final: 0.9133 (mmm) REVERT: H 93 GLU cc_start: 0.8669 (mp0) cc_final: 0.8190 (mp0) REVERT: H 113 GLU cc_start: 0.9268 (tp30) cc_final: 0.8575 (tm-30) outliers start: 14 outliers final: 10 residues processed: 199 average time/residue: 0.1019 time to fit residues: 28.7915 Evaluate side-chains 196 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 185 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 24 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 70 optimal weight: 30.0000 chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 49 optimal weight: 0.0970 chunk 77 optimal weight: 50.0000 chunk 56 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 55 GLN E 85 GLN E 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.061836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.038983 restraints weight = 54268.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.040048 restraints weight = 29781.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.040741 restraints weight = 21892.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.041150 restraints weight = 18699.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.041251 restraints weight = 17230.539| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11330 Z= 0.196 Angle : 0.732 9.358 16385 Z= 0.411 Chirality : 0.046 0.332 1874 Planarity : 0.004 0.049 1197 Dihedral : 32.152 176.377 3499 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.07 % Allowed : 27.29 % Favored : 70.64 % 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: 2.50 (0.31), residues: 681 helix: 2.32 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -0.73 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 78 TYR 0.022 0.002 TYR H 83 PHE 0.014 0.002 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.20 (11330) covalent geometry : angle 0.73217 / 0.41 (16385) hydrogen bonds : bond 0.04927 / 3.32 ( 706) hydrogen bonds : angle 3.33942 / 2.47 ( 1782) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 182 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8888 (mmm-85) cc_final: 0.7969 (mmm-85) REVERT: A 85 GLN cc_start: 0.9112 (mt0) cc_final: 0.8625 (mt0) REVERT: A 94 GLU cc_start: 0.8686 (tp30) cc_final: 0.8416 (tp30) REVERT: A 125 GLN cc_start: 0.9204 (mt0) cc_final: 0.8330 (mp10) REVERT: B 44 LYS cc_start: 0.9052 (mmtt) cc_final: 0.8830 (tppt) REVERT: C 16 THR cc_start: 0.8370 (p) cc_final: 0.8144 (t) REVERT: C 20 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7116 (mtp85) REVERT: C 64 GLU cc_start: 0.8547 (tp30) cc_final: 0.8285 (tp30) REVERT: C 73 ASN cc_start: 0.8970 (t0) cc_final: 0.8542 (t0) REVERT: C 104 GLN cc_start: 0.8614 (mp10) cc_final: 0.7825 (mp10) REVERT: D 46 LYS cc_start: 0.9506 (mmtp) cc_final: 0.9205 (mmmt) REVERT: D 68 ASP cc_start: 0.9092 (t70) cc_final: 0.8822 (t70) REVERT: D 71 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8691 (tm-30) REVERT: D 120 LYS cc_start: 0.9555 (ttpt) cc_final: 0.9157 (ttpp) REVERT: E 63 ARG cc_start: 0.8196 (mmp-170) cc_final: 0.7992 (mmm-85) REVERT: E 79 LYS cc_start: 0.8664 (tmtt) cc_final: 0.7945 (tmtt) REVERT: E 94 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8532 (mm-30) REVERT: E 123 ASP cc_start: 0.8794 (m-30) cc_final: 0.8396 (m-30) REVERT: E 125 GLN cc_start: 0.8594 (tm-30) cc_final: 0.8362 (tm-30) REVERT: F 39 ARG cc_start: 0.9211 (tpp-160) cc_final: 0.8777 (tpp-160) REVERT: F 63 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8480 (mt-10) REVERT: F 73 THR cc_start: 0.9661 (m) cc_final: 0.9451 (p) REVERT: G 57 TYR cc_start: 0.8958 (t80) cc_final: 0.8646 (t80) REVERT: G 59 THR cc_start: 0.9699 (m) cc_final: 0.9352 (t) REVERT: G 64 GLU cc_start: 0.8472 (tp30) cc_final: 0.7725 (tp30) REVERT: G 68 ASN cc_start: 0.9247 (m-40) cc_final: 0.8237 (m-40) REVERT: G 89 ASN cc_start: 0.9387 (m-40) cc_final: 0.9002 (m110) REVERT: G 90 ASP cc_start: 0.8567 (t0) cc_final: 0.8143 (t0) REVERT: G 92 GLU cc_start: 0.9025 (mp0) cc_final: 0.8553 (pm20) REVERT: H 46 LYS cc_start: 0.9460 (mmmt) cc_final: 0.9216 (mmmt) REVERT: H 93 GLU cc_start: 0.8675 (mp0) cc_final: 0.8215 (mp0) REVERT: H 113 GLU cc_start: 0.9265 (tp30) cc_final: 0.8607 (tm-30) outliers start: 12 outliers final: 8 residues processed: 191 average time/residue: 0.0982 time to fit residues: 26.5440 Evaluate side-chains 188 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 179 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 33 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 83 optimal weight: 30.0000 chunk 43 optimal weight: 6.9990 chunk 69 optimal weight: 40.0000 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 71 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.060954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.037986 restraints weight = 54283.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.039027 restraints weight = 29962.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.039701 restraints weight = 22183.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.039909 restraints weight = 19007.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.040247 restraints weight = 17843.317| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11330 Z= 0.259 Angle : 0.764 9.154 16385 Z= 0.424 Chirality : 0.047 0.309 1874 Planarity : 0.004 0.049 1197 Dihedral : 32.192 174.989 3499 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.25 % Allowed : 27.98 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.31), residues: 681 helix: 2.21 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -0.91 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 42 TYR 0.035 0.002 TYR C 57 PHE 0.025 0.002 PHE A 67 HIS 0.006 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.26 (11330) covalent geometry : angle 0.76397 / 0.42 (16385) hydrogen bonds : bond 0.05544 / 3.72 ( 706) hydrogen bonds : angle 3.52622 / 2.59 ( 1782) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8931 (mmm-85) cc_final: 0.7999 (mmm-85) REVERT: A 85 GLN cc_start: 0.9126 (mt0) cc_final: 0.8645 (mt0) REVERT: A 94 GLU cc_start: 0.8699 (tp30) cc_final: 0.8313 (tp30) REVERT: A 125 GLN cc_start: 0.9211 (mt0) cc_final: 0.8358 (mp10) REVERT: B 44 LYS cc_start: 0.9059 (mmtt) cc_final: 0.8839 (tppt) REVERT: C 20 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7014 (mtp85) REVERT: C 64 GLU cc_start: 0.8542 (tp30) cc_final: 0.8272 (tp30) REVERT: C 73 ASN cc_start: 0.8992 (t0) cc_final: 0.8567 (t0) REVERT: C 104 GLN cc_start: 0.8656 (mp10) cc_final: 0.7878 (mp10) REVERT: D 46 LYS cc_start: 0.9491 (mmtp) cc_final: 0.9219 (mmmt) REVERT: D 68 ASP cc_start: 0.9099 (t70) cc_final: 0.8754 (t70) REVERT: D 71 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8736 (tm-30) REVERT: D 120 LYS cc_start: 0.9581 (ttpt) cc_final: 0.9186 (ttpp) REVERT: E 63 ARG cc_start: 0.8256 (mmp-170) cc_final: 0.8037 (mmm-85) REVERT: E 79 LYS cc_start: 0.8716 (tmtt) cc_final: 0.7979 (tmtt) REVERT: E 94 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8556 (mm-30) REVERT: E 105 GLU cc_start: 0.8665 (tt0) cc_final: 0.8381 (tp30) REVERT: E 123 ASP cc_start: 0.8789 (m-30) cc_final: 0.8391 (m-30) REVERT: E 125 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8371 (tm-30) REVERT: F 39 ARG cc_start: 0.9226 (tpp-160) cc_final: 0.8662 (tpp-160) REVERT: F 63 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8502 (mt-10) REVERT: G 57 TYR cc_start: 0.9008 (t80) cc_final: 0.8760 (t80) REVERT: G 59 THR cc_start: 0.9705 (m) cc_final: 0.9349 (t) REVERT: G 64 GLU cc_start: 0.8475 (tp30) cc_final: 0.7658 (tp30) REVERT: G 68 ASN cc_start: 0.9204 (m-40) cc_final: 0.8197 (m-40) REVERT: G 89 ASN cc_start: 0.9382 (m-40) cc_final: 0.8993 (m110) REVERT: G 90 ASP cc_start: 0.8617 (t0) cc_final: 0.8130 (t0) REVERT: G 92 GLU cc_start: 0.9027 (mp0) cc_final: 0.8496 (pm20) REVERT: H 46 LYS cc_start: 0.9481 (mmmt) cc_final: 0.9188 (mmmt) REVERT: H 93 GLU cc_start: 0.8733 (mp0) cc_final: 0.8227 (mp0) REVERT: H 113 GLU cc_start: 0.9291 (tp30) cc_final: 0.8625 (tm-30) outliers start: 13 outliers final: 11 residues processed: 183 average time/residue: 0.0989 time to fit residues: 25.5822 Evaluate side-chains 187 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 69 optimal weight: 40.0000 chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 0.0010 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 83 optimal weight: 30.0000 chunk 77 optimal weight: 50.0000 chunk 87 optimal weight: 30.0000 chunk 35 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 50.0000 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.062100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.039429 restraints weight = 54748.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.040510 restraints weight = 29692.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.041219 restraints weight = 21829.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.041579 restraints weight = 18642.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.041819 restraints weight = 17293.033| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11330 Z= 0.164 Angle : 0.718 9.804 16385 Z= 0.405 Chirality : 0.045 0.319 1874 Planarity : 0.004 0.048 1197 Dihedral : 32.071 176.467 3499 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.42 % Allowed : 28.50 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.45 (0.32), residues: 681 helix: 2.31 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -0.84 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 99 TYR 0.032 0.002 TYR C 57 PHE 0.017 0.002 PHE A 67 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.16 (11330) covalent geometry : angle 0.71756 / 0.41 (16385) hydrogen bonds : bond 0.04585 / 3.07 ( 706) hydrogen bonds : angle 3.34268 / 2.46 ( 1782) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1770.17 seconds wall clock time: 31 minutes 19.81 seconds (1879.81 seconds total)