Starting phenix.real_space_refine on Thu Jul 2 20:52:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dbh_30631/07_2026/7dbh_30631.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dbh_30631/07_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_30631/07_2026/7dbh_30631.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dbh_30631/07_2026/7dbh_30631.map" model { file = "/net/cci-nas-00/data/ceres_data/7dbh_30631/07_2026/7dbh_30631.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dbh_30631/07_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.88, per 1000 atoms: 0.18 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: 0.72 Conformation dependent library (CDL) restraints added in 196.6 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: 1.24 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: 1.87 Time building geometry restraints manager: 1.01 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: 14354 1.25 - 2.50: 1583 2.50 - 3.75: 398 3.75 - 5.00: 38 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: 0.530 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.570 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.610 ------------------------------------------------------------------------------- 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= 0.663 Angle : 0.880 6.252 16385 Z= 0.736 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 0.88037 / 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 : 0.276 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: 0.9057 (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 79 LYS cc_start: 0.9071 (mtmm) cc_final: 0.8831 (mtmm) REVERT: B 80 THR cc_start: 0.9530 (m) cc_final: 0.9200 (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: 0.7987 (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 39 ARG cc_start: 0.9363 (mmt90) cc_final: 0.9163 (tpp-160) 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: 0.8451 (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: 0.8268 (tp30) REVERT: H 46 LYS cc_start: 0.9456 (mmmt) cc_final: 0.9215 (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: 0.1056 time to fit residues: 29.6030 Evaluate side-chains 156 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.199 ------------------------------------------------------------------------------- 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: 10.0000 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: 0.8980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 30.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN B 93 GLN D 49 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.062523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.040199 restraints weight = 53592.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.041369 restraints weight = 27823.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.042106 restraints weight = 19946.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.042329 restraints weight = 16861.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.042329 restraints weight = 15685.853| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11330 Z= 0.176 Angle : 0.769 9.651 16385 Z= 0.445 Chirality : 0.050 0.388 1874 Planarity : 0.005 0.035 1197 Dihedral : 32.476 174.960 3499 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.90 % Allowed : 12.44 % Favored : 85.66 % 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 : -1.09 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 63 TYR 0.050 0.003 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 0.00302 / 0.18 (11330) covalent geometry : angle 0.76888 / 0.45 (16385) hydrogen bonds : bond 0.05500 / 3.78 ( 706) hydrogen bonds : angle 3.72406 / 2.78 ( 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 222 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 211 time to evaluate : 0.273 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 65 LEU cc_start: 0.9786 (tp) cc_final: 0.9583 (tt) REVERT: A 79 LYS cc_start: 0.9149 (tptp) cc_final: 0.8623 (tmtt) REVERT: A 85 GLN cc_start: 0.9325 (mt0) cc_final: 0.8886 (mt0) REVERT: A 94 GLU cc_start: 0.8618 (tp30) cc_final: 0.8287 (tp30) REVERT: A 97 GLU cc_start: 0.8438 (tt0) cc_final: 0.8193 (tt0) REVERT: A 124 THR cc_start: 0.9706 (m) cc_final: 0.9287 (p) REVERT: A 125 GLN cc_start: 0.9105 (mt0) cc_final: 0.8682 (mt0) REVERT: B 44 LYS cc_start: 0.8965 (mmmt) cc_final: 0.8663 (mmmt) REVERT: B 49 LEU cc_start: 0.9678 (mp) cc_final: 0.9164 (mt) REVERT: B 96 THR cc_start: 0.9490 (m) cc_final: 0.9216 (t) REVERT: C 24 GLN cc_start: 0.9374 (mm110) cc_final: 0.8886 (mp10) REVERT: C 38 ASN cc_start: 0.8439 (t0) cc_final: 0.8000 (t0) REVERT: C 64 GLU cc_start: 0.8667 (tp30) cc_final: 0.8228 (tp30) REVERT: C 104 GLN cc_start: 0.8588 (mp10) cc_final: 0.7737 (mp10) REVERT: D 68 ASP cc_start: 0.8968 (t70) cc_final: 0.8611 (t70) REVERT: D 71 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8604 (tm-30) REVERT: E 125 GLN cc_start: 0.8368 (tm-30) cc_final: 0.8129 (tm-30) REVERT: F 39 ARG cc_start: 0.9224 (mmt90) cc_final: 0.8949 (tpp-160) REVERT: F 44 LYS cc_start: 0.9283 (mtpp) cc_final: 0.8955 (mmmm) REVERT: F 52 GLU cc_start: 0.8688 (tp30) cc_final: 0.8402 (tm-30) REVERT: F 73 THR cc_start: 0.9643 (m) cc_final: 0.9355 (p) REVERT: G 57 TYR cc_start: 0.9009 (t80) cc_final: 0.8525 (t80) REVERT: G 64 GLU cc_start: 0.8747 (tp30) cc_final: 0.8162 (tp30) REVERT: G 89 ASN cc_start: 0.9349 (m-40) cc_final: 0.9076 (m110) REVERT: H 46 LYS cc_start: 0.9380 (mmmt) cc_final: 0.9170 (mmmt) REVERT: H 71 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8558 (tm-30) REVERT: H 93 GLU cc_start: 0.8444 (mp0) cc_final: 0.8139 (mp0) REVERT: H 113 GLU cc_start: 0.9149 (tp30) cc_final: 0.8741 (tt0) outliers start: 11 outliers final: 6 residues processed: 215 average time/residue: 0.0861 time to fit residues: 26.3685 Evaluate side-chains 181 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 175 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER 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: 0.6980 chunk 54 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 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: 2.9990 chunk 73 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS 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 = 0.061837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.039213 restraints weight = 54771.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.040302 restraints weight = 29834.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.041011 restraints weight = 21858.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.041397 restraints weight = 18633.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.041477 restraints weight = 17225.815| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11330 Z= 0.194 Angle : 0.710 8.886 16385 Z= 0.416 Chirality : 0.046 0.345 1874 Planarity : 0.004 0.052 1197 Dihedral : 32.432 177.799 3499 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.76 % Allowed : 17.79 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.31), residues: 681 helix: 2.29 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -0.95 (0.45), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 92 TYR 0.033 0.002 TYR D 83 PHE 0.015 0.002 PHE E 78 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.19 (11330) covalent geometry : angle 0.70985 / 0.42 (16385) hydrogen bonds : bond 0.05467 / 3.72 ( 706) hydrogen bonds : angle 3.54942 / 2.63 ( 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 195 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.9224 (mt0) cc_final: 0.8744 (mt0) REVERT: A 94 GLU cc_start: 0.8674 (tp30) cc_final: 0.8394 (tp30) REVERT: A 97 GLU cc_start: 0.8500 (tt0) cc_final: 0.8228 (tt0) REVERT: A 125 GLN cc_start: 0.9226 (mt0) cc_final: 0.8414 (mp10) REVERT: B 44 LYS cc_start: 0.9007 (mmmt) cc_final: 0.8733 (mmmt) REVERT: B 96 THR cc_start: 0.9523 (m) cc_final: 0.9212 (p) REVERT: C 38 ASN cc_start: 0.8404 (t0) cc_final: 0.7941 (t0) REVERT: C 64 GLU cc_start: 0.8618 (tp30) cc_final: 0.8261 (tp30) REVERT: C 104 GLN cc_start: 0.8564 (mp10) cc_final: 0.8032 (mp10) REVERT: D 46 LYS cc_start: 0.9563 (mmtp) cc_final: 0.9307 (mmtp) REVERT: D 68 ASP cc_start: 0.9060 (t70) cc_final: 0.8729 (t70) REVERT: D 71 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8623 (tm-30) REVERT: D 120 LYS cc_start: 0.9518 (ttpt) cc_final: 0.9126 (ttpp) REVERT: E 125 GLN cc_start: 0.8430 (tm130) cc_final: 0.8108 (tm-30) REVERT: F 44 LYS cc_start: 0.9275 (mtpp) cc_final: 0.9011 (mmmm) REVERT: F 52 GLU cc_start: 0.8682 (tp30) cc_final: 0.8343 (tm-30) REVERT: F 63 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8361 (mt-10) REVERT: F 73 THR cc_start: 0.9646 (m) cc_final: 0.9396 (p) REVERT: G 39 TYR cc_start: 0.9263 (m-80) cc_final: 0.9022 (m-80) REVERT: G 57 TYR cc_start: 0.9074 (t80) cc_final: 0.8563 (t80) REVERT: G 64 GLU cc_start: 0.8714 (tp30) cc_final: 0.8073 (tp30) REVERT: G 89 ASN cc_start: 0.9360 (m-40) cc_final: 0.9055 (m110) REVERT: G 90 ASP cc_start: 0.8377 (t0) cc_final: 0.8071 (t0) REVERT: G 92 GLU cc_start: 0.8948 (mp0) cc_final: 0.8461 (pm20) REVERT: H 46 LYS cc_start: 0.9407 (mmmt) cc_final: 0.9186 (mmmt) REVERT: H 71 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8578 (tm-30) REVERT: H 93 GLU cc_start: 0.8602 (mp0) cc_final: 0.8322 (mp0) REVERT: H 113 GLU cc_start: 0.9164 (tp30) cc_final: 0.8742 (tt0) outliers start: 16 outliers final: 12 residues processed: 184 average time/residue: 0.0836 time to fit residues: 21.8241 Evaluate side-chains 177 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 0.176 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 5 optimal weight: 10.0000 chunk 69 optimal weight: 40.0000 chunk 16 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 overall best weight: 3.7986 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.061508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.038875 restraints weight = 55329.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.039961 restraints weight = 30256.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.040656 restraints weight = 22231.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.040882 restraints weight = 19012.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.041220 restraints weight = 17713.159| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11330 Z= 0.206 Angle : 0.704 8.963 16385 Z= 0.410 Chirality : 0.046 0.346 1874 Planarity : 0.004 0.037 1197 Dihedral : 32.422 179.228 3499 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.63 % Allowed : 18.83 % Favored : 77.55 % 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: 2.33 (0.31), residues: 681 helix: 2.23 (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 0.001 ARG D 92 TYR 0.031 0.002 TYR D 83 PHE 0.012 0.002 PHE E 78 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.21 (11330) covalent geometry : angle 0.70375 / 0.41 (16385) hydrogen bonds : bond 0.05297 / 3.59 ( 706) hydrogen bonds : angle 3.51080 / 2.60 ( 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 209 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.170 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: A 85 GLN cc_start: 0.9208 (mt0) cc_final: 0.8692 (mt0) REVERT: A 94 GLU cc_start: 0.8693 (tp30) cc_final: 0.8412 (tp30) REVERT: A 97 GLU cc_start: 0.8501 (tt0) cc_final: 0.8223 (tt0) REVERT: A 125 GLN cc_start: 0.9219 (mt0) cc_final: 0.8380 (mp10) REVERT: B 96 THR cc_start: 0.9531 (m) cc_final: 0.9248 (p) REVERT: C 24 GLN cc_start: 0.9333 (mm110) cc_final: 0.9106 (mp10) REVERT: C 38 ASN cc_start: 0.8378 (t0) cc_final: 0.7928 (t0) REVERT: C 64 GLU cc_start: 0.8621 (tp30) cc_final: 0.8288 (tp30) REVERT: C 73 ASN cc_start: 0.8912 (t0) cc_final: 0.8562 (t0) REVERT: C 104 GLN cc_start: 0.8618 (mp10) cc_final: 0.7978 (mp10) REVERT: D 46 LYS cc_start: 0.9543 (mmtp) cc_final: 0.9297 (mmtp) REVERT: D 68 ASP cc_start: 0.9083 (t70) cc_final: 0.8741 (t70) REVERT: D 71 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8626 (tm-30) REVERT: D 120 LYS cc_start: 0.9523 (ttpt) cc_final: 0.9141 (ttpp) REVERT: E 79 LYS cc_start: 0.8612 (tmtt) cc_final: 0.7972 (tmtt) REVERT: E 123 ASP cc_start: 0.8913 (m-30) cc_final: 0.8481 (m-30) REVERT: E 125 GLN cc_start: 0.8484 (tm130) cc_final: 0.8149 (tm-30) REVERT: F 39 ARG cc_start: 0.9175 (tpp-160) cc_final: 0.8610 (tpp80) REVERT: F 52 GLU cc_start: 0.8682 (tp30) cc_final: 0.8334 (tm-30) REVERT: F 63 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8537 (mt-10) REVERT: F 73 THR cc_start: 0.9644 (m) cc_final: 0.9415 (p) REVERT: G 39 TYR cc_start: 0.9270 (m-80) cc_final: 0.9014 (m-80) REVERT: G 57 TYR cc_start: 0.9073 (t80) cc_final: 0.8659 (t80) REVERT: G 64 GLU cc_start: 0.8701 (tp30) cc_final: 0.7943 (tp30) REVERT: G 68 ASN cc_start: 0.9240 (m-40) cc_final: 0.8557 (m-40) REVERT: G 89 ASN cc_start: 0.9356 (m-40) cc_final: 0.9026 (m110) REVERT: H 46 LYS cc_start: 0.9424 (mmmt) cc_final: 0.9185 (mmmt) REVERT: H 71 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8582 (tm-30) REVERT: H 93 GLU cc_start: 0.8544 (mp0) cc_final: 0.8221 (mp0) outliers start: 21 outliers final: 15 residues processed: 196 average time/residue: 0.0811 time to fit residues: 22.6047 Evaluate side-chains 186 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.174 ------------------------------------------------------------------------------- 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 E residue 86 SER 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 Chi-restraints excluded: chain H residue 90 THR 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: 0.8980 chunk 27 optimal weight: 1.9990 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: 3.9990 overall best weight: 11.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 94 ASN E 55 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.058919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.036367 restraints weight = 55819.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.037392 restraints weight = 31119.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.038028 restraints weight = 23090.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.038382 restraints weight = 19860.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.038493 restraints weight = 18384.114| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.061 11330 Z= 0.466 Angle : 0.887 10.864 16385 Z= 0.488 Chirality : 0.051 0.325 1874 Planarity : 0.005 0.040 1197 Dihedral : 32.638 175.918 3499 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.66 % Allowed : 20.21 % Favored : 75.13 % 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: 1.71 (0.31), residues: 681 helix: 1.79 (0.21), residues: 528 sheet: None (None), residues: 0 loop : -1.22 (0.45), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 42 TYR 0.051 0.003 TYR D 83 PHE 0.022 0.003 PHE E 78 HIS 0.007 0.002 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00940 / 0.47 (11330) covalent geometry : angle 0.88706 / 0.49 (16385) hydrogen bonds : bond 0.08346 / 5.65 ( 706) hydrogen bonds : angle 4.10652 / 3.03 ( 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 178 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.236 Fit side-chains 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: 0.8707 (mt0) REVERT: A 94 GLU cc_start: 0.8839 (tp30) cc_final: 0.8576 (tp30) REVERT: A 97 GLU cc_start: 0.8488 (tt0) cc_final: 0.8284 (tt0) REVERT: A 125 GLN cc_start: 0.9221 (mt0) cc_final: 0.8480 (mp10) REVERT: C 38 ASN cc_start: 0.8457 (t0) cc_final: 0.8074 (t0) REVERT: C 64 GLU cc_start: 0.8585 (tp30) cc_final: 0.8297 (tp30) REVERT: C 104 GLN cc_start: 0.8729 (mp10) cc_final: 0.8052 (mp10) REVERT: D 46 LYS cc_start: 0.9526 (mmtp) cc_final: 0.9304 (mmmt) REVERT: D 68 ASP cc_start: 0.9124 (t70) cc_final: 0.8549 (t0) REVERT: E 79 LYS cc_start: 0.8734 (tmtt) cc_final: 0.8115 (tmtt) REVERT: E 125 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8349 (tm-30) REVERT: F 39 ARG cc_start: 0.9182 (tpp-160) cc_final: 0.8837 (tpp-160) REVERT: F 44 LYS cc_start: 0.9276 (mtpp) cc_final: 0.9021 (mmmm) REVERT: F 52 GLU cc_start: 0.8825 (tp30) cc_final: 0.8404 (tm-30) REVERT: F 63 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8604 (mt-10) REVERT: F 85 ASP cc_start: 0.9023 (m-30) cc_final: 0.8786 (m-30) REVERT: G 38 ASN cc_start: 0.9262 (m-40) cc_final: 0.8898 (m110) REVERT: G 57 TYR cc_start: 0.9114 (t80) cc_final: 0.8854 (t80) REVERT: G 64 GLU cc_start: 0.8638 (tp30) cc_final: 0.7854 (tp30) REVERT: G 89 ASN cc_start: 0.9378 (m-40) cc_final: 0.9044 (m110) REVERT: H 93 GLU cc_start: 0.8729 (mp0) cc_final: 0.8269 (mp0) REVERT: H 113 GLU cc_start: 0.9333 (tp30) cc_final: 0.8641 (tm-30) outliers start: 27 outliers final: 24 residues processed: 166 average time/residue: 0.0850 time to fit residues: 19.9947 Evaluate side-chains 172 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 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 39 ILE 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 60 VAL 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 G residue 100 VAL 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: 0.9990 chunk 3 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 70 optimal weight: 30.0000 chunk 4 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN E 85 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.061769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.038980 restraints weight = 54321.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.040100 restraints weight = 28466.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.040834 restraints weight = 20735.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.041226 restraints weight = 17676.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.041328 restraints weight = 16339.928| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11330 Z= 0.162 Angle : 0.700 8.512 16385 Z= 0.407 Chirality : 0.047 0.343 1874 Planarity : 0.004 0.043 1197 Dihedral : 32.502 178.314 3499 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.94 % Allowed : 22.80 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.31), residues: 681 helix: 2.31 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -0.84 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 72 TYR 0.019 0.002 TYR H 83 PHE 0.013 0.002 PHE H 70 HIS 0.005 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.16 (11330) covalent geometry : angle 0.69994 / 0.41 (16385) hydrogen bonds : bond 0.04975 / 3.32 ( 706) hydrogen bonds : angle 3.44184 / 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 206 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.9184 (mt0) cc_final: 0.8555 (mt0) REVERT: A 94 GLU cc_start: 0.8709 (tp30) cc_final: 0.8495 (tp30) REVERT: A 97 GLU cc_start: 0.8459 (tt0) cc_final: 0.8170 (tt0) REVERT: A 125 GLN cc_start: 0.9181 (mt0) cc_final: 0.8345 (mp10) REVERT: B 84 MET cc_start: 0.9175 (tpp) cc_final: 0.8632 (mmm) REVERT: B 96 THR cc_start: 0.9491 (m) cc_final: 0.9204 (p) REVERT: C 20 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.6985 (mtp85) REVERT: C 24 GLN cc_start: 0.9315 (mm110) cc_final: 0.9107 (mp10) REVERT: C 38 ASN cc_start: 0.8378 (t0) cc_final: 0.7856 (t0) REVERT: C 64 GLU cc_start: 0.8691 (tp30) cc_final: 0.8346 (tp30) REVERT: C 73 ASN cc_start: 0.8954 (t0) cc_final: 0.8518 (t0) REVERT: C 104 GLN cc_start: 0.8611 (mp10) cc_final: 0.7828 (mp10) REVERT: D 46 LYS cc_start: 0.9515 (mmtp) cc_final: 0.9263 (mmmt) REVERT: D 68 ASP cc_start: 0.9064 (t70) cc_final: 0.8716 (t70) REVERT: D 71 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8697 (tm-30) REVERT: D 120 LYS cc_start: 0.9532 (ttpt) cc_final: 0.9142 (ttpp) REVERT: E 79 LYS cc_start: 0.8587 (tmtt) cc_final: 0.7886 (tmtt) REVERT: E 85 GLN cc_start: 0.9135 (mt0) cc_final: 0.8886 (mt0) REVERT: E 93 GLN cc_start: 0.9131 (tp-100) cc_final: 0.8777 (tp40) REVERT: E 123 ASP cc_start: 0.8842 (m-30) cc_final: 0.8448 (m-30) REVERT: E 125 GLN cc_start: 0.8558 (tm-30) cc_final: 0.8324 (tm-30) REVERT: F 39 ARG cc_start: 0.9150 (tpp-160) cc_final: 0.8684 (tpp-160) REVERT: F 52 GLU cc_start: 0.8668 (tp30) cc_final: 0.8307 (tm-30) REVERT: F 63 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8496 (mt-10) REVERT: F 73 THR cc_start: 0.9661 (m) cc_final: 0.9428 (p) REVERT: G 38 ASN cc_start: 0.8941 (m-40) cc_final: 0.8660 (m110) REVERT: G 64 GLU cc_start: 0.8628 (tp30) cc_final: 0.7825 (tp30) REVERT: G 68 ASN cc_start: 0.9227 (m-40) cc_final: 0.8369 (m-40) REVERT: G 89 ASN cc_start: 0.9394 (m-40) cc_final: 0.9037 (m110) REVERT: G 90 ASP cc_start: 0.8458 (t0) cc_final: 0.8154 (t0) REVERT: G 92 GLU cc_start: 0.9004 (mp0) cc_final: 0.8603 (pm20) REVERT: H 93 GLU cc_start: 0.8627 (mp0) cc_final: 0.8188 (mp0) outliers start: 17 outliers final: 11 residues processed: 197 average time/residue: 0.0864 time to fit residues: 24.2702 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 : 0.265 ------------------------------------------------------------------------------- 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 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 G residue 16 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 100 VAL 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: 0.9990 chunk 58 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 33 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 86 optimal weight: 40.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.062011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.039791 restraints weight = 53630.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.040898 restraints weight = 28013.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.041603 restraints weight = 20289.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.041995 restraints weight = 17232.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.042104 restraints weight = 15864.456| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2938 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= 0.156 Angle : 0.689 8.266 16385 Z= 0.400 Chirality : 0.046 0.316 1874 Planarity : 0.004 0.042 1197 Dihedral : 32.331 177.026 3499 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.90 % Allowed : 24.01 % Favored : 74.09 % 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: 2.71 (0.31), residues: 681 helix: 2.44 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -0.48 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 63 TYR 0.021 0.002 TYR G 57 PHE 0.012 0.002 PHE H 70 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.16 (11330) covalent geometry : angle 0.68920 / 0.40 (16385) hydrogen bonds : bond 0.04756 / 3.22 ( 706) hydrogen bonds : angle 3.33054 / 2.46 ( 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 206 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 195 time to evaluate : 0.220 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: 0.9734 (tt) cc_final: 0.9516 (tt) REVERT: A 81 ASP cc_start: 0.8431 (m-30) cc_final: 0.8012 (p0) REVERT: A 85 GLN cc_start: 0.9145 (mt0) cc_final: 0.8601 (mt0) REVERT: A 94 GLU cc_start: 0.8700 (tp30) cc_final: 0.8464 (tp30) REVERT: A 97 GLU cc_start: 0.8495 (tt0) cc_final: 0.8011 (tt0) REVERT: A 125 GLN cc_start: 0.9216 (mt0) cc_final: 0.8379 (mp10) REVERT: B 84 MET cc_start: 0.9160 (tpp) cc_final: 0.8706 (mmm) REVERT: C 20 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.6977 (mtp85) REVERT: C 64 GLU cc_start: 0.8651 (tp30) cc_final: 0.8366 (tp30) REVERT: C 73 ASN cc_start: 0.8938 (t0) cc_final: 0.8505 (t0) REVERT: C 104 GLN cc_start: 0.8559 (mp10) cc_final: 0.7894 (mp10) REVERT: D 46 LYS cc_start: 0.9530 (mmtp) cc_final: 0.9238 (mmmt) REVERT: D 68 ASP cc_start: 0.9105 (t70) cc_final: 0.8830 (t70) REVERT: D 71 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8713 (tm-30) REVERT: D 120 LYS cc_start: 0.9535 (ttpt) cc_final: 0.9141 (ttpp) REVERT: E 79 LYS cc_start: 0.8584 (tmtt) cc_final: 0.7896 (tmtt) REVERT: E 123 ASP cc_start: 0.8851 (m-30) cc_final: 0.8427 (m-30) REVERT: E 125 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8323 (tm-30) REVERT: F 39 ARG cc_start: 0.9199 (tpp-160) cc_final: 0.8692 (tpp-160) REVERT: F 63 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8481 (mt-10) REVERT: F 73 THR cc_start: 0.9659 (m) cc_final: 0.9453 (p) REVERT: G 57 TYR cc_start: 0.8950 (t80) cc_final: 0.8366 (t80) REVERT: G 64 GLU cc_start: 0.8591 (tp30) cc_final: 0.7739 (tp30) REVERT: G 68 ASN cc_start: 0.9264 (m-40) cc_final: 0.8294 (m-40) REVERT: G 89 ASN cc_start: 0.9370 (m-40) cc_final: 0.8981 (m110) REVERT: G 90 ASP cc_start: 0.8341 (t0) cc_final: 0.8075 (t0) REVERT: G 92 GLU cc_start: 0.9049 (mp0) cc_final: 0.8614 (pm20) REVERT: H 93 GLU cc_start: 0.8683 (mp0) cc_final: 0.8218 (mp0) REVERT: H 113 GLU cc_start: 0.9271 (tp30) cc_final: 0.8824 (tt0) outliers start: 11 outliers final: 8 residues processed: 201 average time/residue: 0.0850 time to fit residues: 24.2703 Evaluate side-chains 185 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 176 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 G residue 16 THR Chi-restraints excluded: chain G residue 61 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 66 optimal weight: 50.0000 chunk 80 optimal weight: 40.0000 chunk 51 optimal weight: 0.9980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.061630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.038867 restraints weight = 54470.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.039906 restraints weight = 30006.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.040581 restraints weight = 22206.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.040989 restraints weight = 19050.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.041160 restraints weight = 17593.308| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11330 Z= 0.200 Angle : 0.710 8.852 16385 Z= 0.407 Chirality : 0.046 0.303 1874 Planarity : 0.004 0.048 1197 Dihedral : 32.323 176.728 3499 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.07 % Allowed : 25.91 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.31), residues: 681 helix: 2.36 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -0.58 (0.46), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 63 TYR 0.021 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 0.00385 / 0.20 (11330) covalent geometry : angle 0.70953 / 0.41 (16385) hydrogen bonds : bond 0.05026 / 3.39 ( 706) hydrogen bonds : angle 3.37943 / 2.49 ( 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 184 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8396 (m-30) cc_final: 0.7956 (p0) REVERT: A 85 GLN cc_start: 0.9140 (mt0) cc_final: 0.8593 (mt0) REVERT: A 94 GLU cc_start: 0.8682 (tp30) cc_final: 0.8424 (tp30) REVERT: A 97 GLU cc_start: 0.8400 (tt0) cc_final: 0.8049 (tt0) REVERT: A 125 GLN cc_start: 0.9224 (mt0) cc_final: 0.8400 (mp10) REVERT: B 30 THR cc_start: 0.9111 (p) cc_final: 0.8893 (t) REVERT: C 20 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.6966 (mtp85) REVERT: C 64 GLU cc_start: 0.8562 (tp30) cc_final: 0.8297 (tp30) REVERT: C 73 ASN cc_start: 0.8955 (t0) cc_final: 0.8514 (t0) REVERT: C 104 GLN cc_start: 0.8614 (mp10) cc_final: 0.7836 (mp10) REVERT: D 46 LYS cc_start: 0.9516 (mmtp) cc_final: 0.9222 (mmmt) REVERT: D 68 ASP cc_start: 0.9096 (t70) cc_final: 0.8824 (t70) REVERT: D 71 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8708 (tm-30) REVERT: D 120 LYS cc_start: 0.9549 (ttpt) cc_final: 0.9154 (ttpp) REVERT: E 79 LYS cc_start: 0.8661 (tmtt) cc_final: 0.7935 (tmtt) REVERT: E 94 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8499 (mm-30) REVERT: E 123 ASP cc_start: 0.8821 (m-30) cc_final: 0.8396 (m-30) REVERT: E 125 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8360 (tm-30) REVERT: F 39 ARG cc_start: 0.9170 (tpp-160) cc_final: 0.8641 (tpp-160) REVERT: F 63 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8484 (mt-10) REVERT: G 38 ASN cc_start: 0.8934 (OUTLIER) cc_final: 0.8671 (m-40) REVERT: G 57 TYR cc_start: 0.8987 (t80) cc_final: 0.8581 (t80) REVERT: G 64 GLU cc_start: 0.8516 (tp30) cc_final: 0.7667 (tp30) REVERT: G 68 ASN cc_start: 0.9258 (m-40) cc_final: 0.8269 (m-40) REVERT: G 89 ASN cc_start: 0.9365 (m-40) cc_final: 0.8998 (m110) REVERT: G 90 ASP cc_start: 0.8481 (t0) cc_final: 0.8155 (t0) REVERT: G 92 GLU cc_start: 0.9010 (mp0) cc_final: 0.8591 (pm20) REVERT: H 93 GLU cc_start: 0.8663 (mp0) cc_final: 0.8217 (mp0) REVERT: H 113 GLU cc_start: 0.9263 (tp30) cc_final: 0.8596 (tm-30) outliers start: 12 outliers final: 8 residues processed: 179 average time/residue: 0.0937 time to fit residues: 23.6268 Evaluate side-chains 174 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 164 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 A residue 124 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 38 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 24 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 70 optimal weight: 40.0000 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 77 optimal weight: 50.0000 chunk 56 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN G 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.061796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.039025 restraints weight = 54711.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.040025 restraints weight = 30077.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.040697 restraints weight = 22235.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.041085 restraints weight = 19082.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.041201 restraints weight = 17656.211| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11330 Z= 0.192 Angle : 0.713 8.820 16385 Z= 0.407 Chirality : 0.045 0.300 1874 Planarity : 0.004 0.048 1197 Dihedral : 32.287 176.971 3499 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.25 % Allowed : 26.25 % Favored : 71.50 % 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 (0.31), residues: 681 helix: 2.30 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -0.69 (0.46), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 63 TYR 0.022 0.002 TYR H 83 PHE 0.018 0.002 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.19 (11330) covalent geometry : angle 0.71338 / 0.41 (16385) hydrogen bonds : bond 0.04854 / 3.27 ( 706) hydrogen bonds : angle 3.35923 / 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 188 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 0.253 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: 0.9130 (mt0) cc_final: 0.8579 (mt0) REVERT: A 94 GLU cc_start: 0.8697 (tp30) cc_final: 0.8399 (tp30) REVERT: A 97 GLU cc_start: 0.8426 (tt0) cc_final: 0.8111 (tt0) REVERT: A 125 GLN cc_start: 0.9211 (mt0) cc_final: 0.8338 (mp10) REVERT: B 30 THR cc_start: 0.9097 (p) cc_final: 0.8883 (t) REVERT: C 20 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6989 (mtp85) REVERT: C 38 ASN cc_start: 0.8399 (t0) cc_final: 0.7793 (t0) REVERT: C 64 GLU cc_start: 0.8538 (tp30) cc_final: 0.8286 (tp30) REVERT: C 73 ASN cc_start: 0.8962 (t0) cc_final: 0.8532 (t0) REVERT: C 104 GLN cc_start: 0.8626 (mp10) cc_final: 0.7845 (mp10) REVERT: D 46 LYS cc_start: 0.9507 (mmtp) cc_final: 0.9208 (mmmt) REVERT: D 68 ASP cc_start: 0.9085 (t70) cc_final: 0.8812 (t70) REVERT: D 71 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8684 (tm-30) REVERT: D 120 LYS cc_start: 0.9550 (ttpt) cc_final: 0.9158 (ttpp) REVERT: E 79 LYS cc_start: 0.8676 (tmtt) cc_final: 0.7949 (tmtt) REVERT: E 94 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8517 (mm-30) REVERT: E 123 ASP cc_start: 0.8806 (m-30) cc_final: 0.8397 (m-30) REVERT: E 125 GLN cc_start: 0.8594 (tm-30) cc_final: 0.8363 (tm-30) REVERT: F 39 ARG cc_start: 0.9172 (tpp-160) cc_final: 0.8636 (tpp-160) REVERT: F 63 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8482 (mt-10) REVERT: F 85 ASP cc_start: 0.8576 (m-30) cc_final: 0.8367 (m-30) REVERT: G 38 ASN cc_start: 0.9051 (OUTLIER) cc_final: 0.8587 (m-40) REVERT: G 57 TYR cc_start: 0.9004 (t80) cc_final: 0.8630 (t80) REVERT: G 59 THR cc_start: 0.9695 (m) cc_final: 0.9340 (t) REVERT: G 64 GLU cc_start: 0.8479 (tp30) cc_final: 0.7732 (tp30) REVERT: G 68 ASN cc_start: 0.9243 (m-40) cc_final: 0.8236 (m-40) REVERT: G 89 ASN cc_start: 0.9365 (m-40) cc_final: 0.8993 (m110) REVERT: G 90 ASP cc_start: 0.8517 (t0) cc_final: 0.8090 (t0) REVERT: G 92 GLU cc_start: 0.9001 (mp0) cc_final: 0.8576 (pm20) REVERT: H 93 GLU cc_start: 0.8655 (mp0) cc_final: 0.8191 (mp0) REVERT: H 113 GLU cc_start: 0.9262 (tp30) cc_final: 0.8599 (tm-30) outliers start: 13 outliers final: 10 residues processed: 182 average time/residue: 0.0893 time to fit residues: 23.2009 Evaluate side-chains 185 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 173 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS 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 130 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 38 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 33 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 30.0000 chunk 43 optimal weight: 7.9990 chunk 69 optimal weight: 30.0000 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 71 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.061551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.038712 restraints weight = 54625.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.039771 restraints weight = 30182.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.040456 restraints weight = 22241.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.040843 restraints weight = 19066.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.040955 restraints weight = 17661.867| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11330 Z= 0.207 Angle : 0.721 9.182 16385 Z= 0.409 Chirality : 0.045 0.288 1874 Planarity : 0.004 0.048 1197 Dihedral : 32.260 176.421 3499 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.59 % Allowed : 26.60 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.31), residues: 681 helix: 2.27 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -0.76 (0.45), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 63 TYR 0.022 0.002 TYR H 83 PHE 0.016 0.002 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.21 (11330) covalent geometry : angle 0.72142 / 0.41 (16385) hydrogen bonds : bond 0.04978 / 3.34 ( 706) hydrogen bonds : angle 3.36313 / 2.47 ( 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 187 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.9129 (mt0) cc_final: 0.8578 (mt0) REVERT: A 94 GLU cc_start: 0.8687 (tp30) cc_final: 0.8350 (tp30) REVERT: A 97 GLU cc_start: 0.8432 (tt0) cc_final: 0.8110 (tt0) REVERT: A 125 GLN cc_start: 0.9207 (mt0) cc_final: 0.8341 (mp10) REVERT: B 30 THR cc_start: 0.9106 (p) cc_final: 0.8890 (t) REVERT: B 44 LYS cc_start: 0.9042 (mmtt) cc_final: 0.8792 (tppt) REVERT: B 88 TYR cc_start: 0.9017 (m-80) cc_final: 0.8750 (m-80) REVERT: C 20 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.6976 (mtp85) REVERT: C 38 ASN cc_start: 0.8386 (t0) cc_final: 0.7835 (t0) REVERT: C 64 GLU cc_start: 0.8533 (tp30) cc_final: 0.8295 (tp30) REVERT: C 73 ASN cc_start: 0.8976 (t0) cc_final: 0.8543 (t0) REVERT: C 104 GLN cc_start: 0.8628 (mp10) cc_final: 0.7843 (mp10) REVERT: D 46 LYS cc_start: 0.9495 (mmtp) cc_final: 0.9199 (mmmt) REVERT: D 68 ASP cc_start: 0.9093 (t70) cc_final: 0.8829 (t70) REVERT: D 71 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8718 (tm-30) REVERT: D 120 LYS cc_start: 0.9556 (ttpt) cc_final: 0.9166 (ttpp) REVERT: E 79 LYS cc_start: 0.8686 (tmtt) cc_final: 0.7952 (tmtt) REVERT: E 94 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8524 (mm-30) REVERT: E 123 ASP cc_start: 0.8764 (m-30) cc_final: 0.8383 (m-30) REVERT: E 125 GLN cc_start: 0.8604 (tm-30) cc_final: 0.8384 (tm-30) REVERT: F 39 ARG cc_start: 0.9213 (tpp-160) cc_final: 0.8640 (tpp-160) REVERT: F 63 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8488 (mt-10) REVERT: G 38 ASN cc_start: 0.9111 (m-40) cc_final: 0.8678 (m-40) REVERT: G 57 TYR cc_start: 0.9002 (t80) cc_final: 0.8635 (t80) REVERT: G 59 THR cc_start: 0.9696 (m) cc_final: 0.9347 (t) REVERT: G 64 GLU cc_start: 0.8491 (tp30) cc_final: 0.7702 (tp30) REVERT: G 68 ASN cc_start: 0.9234 (m-40) cc_final: 0.8220 (m-40) REVERT: G 89 ASN cc_start: 0.9368 (m-40) cc_final: 0.8996 (m110) REVERT: G 90 ASP cc_start: 0.8515 (t0) cc_final: 0.8056 (t0) REVERT: G 92 GLU cc_start: 0.8987 (mp0) cc_final: 0.8552 (pm20) REVERT: H 37 TYR cc_start: 0.9536 (m-80) cc_final: 0.9267 (m-80) REVERT: H 93 GLU cc_start: 0.8662 (mp0) cc_final: 0.8218 (mp0) REVERT: H 113 GLU cc_start: 0.9268 (tp30) cc_final: 0.8605 (tm-30) outliers start: 15 outliers final: 11 residues processed: 181 average time/residue: 0.0886 time to fit residues: 22.7478 Evaluate side-chains 182 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 170 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS 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 130 ILE Chi-restraints excluded: chain G residue 16 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: 6.9990 chunk 14 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 83 optimal weight: 30.0000 chunk 77 optimal weight: 50.0000 chunk 87 optimal weight: 30.0000 chunk 35 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 50.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.061155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.038220 restraints weight = 55227.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.039268 restraints weight = 30679.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.039943 restraints weight = 22722.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.040334 restraints weight = 19467.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.040444 restraints weight = 18015.343| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11330 Z= 0.230 Angle : 0.735 9.203 16385 Z= 0.414 Chirality : 0.045 0.278 1874 Planarity : 0.004 0.048 1197 Dihedral : 32.259 175.274 3499 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.42 % Allowed : 27.12 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.31), residues: 681 helix: 2.22 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -0.77 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 63 TYR 0.021 0.002 TYR H 83 PHE 0.016 0.002 PHE A 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.23 (11330) covalent geometry : angle 0.73453 / 0.41 (16385) hydrogen bonds : bond 0.05289 / 3.55 ( 706) hydrogen bonds : angle 3.41564 / 2.51 ( 1782) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1520.06 seconds wall clock time: 26 minutes 59.92 seconds (1619.92 seconds total)