Starting phenix.real_space_refine on Wed Sep 17 17:10:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ybk_39120/09_2025/8ybk_39120.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ybk_39120/09_2025/8ybk_39120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ybk_39120/09_2025/8ybk_39120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ybk_39120/09_2025/8ybk_39120.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ybk_39120/09_2025/8ybk_39120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ybk_39120/09_2025/8ybk_39120.map" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 228 5.49 5 S 14 5.16 5 C 5726 2.51 5 N 1932 2.21 5 O 2361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10261 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 632 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 764 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 773 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2321 Classifications: {'DNA': 114} Link IDs: {'rna3p': 113} Chain: "J" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2353 Classifications: {'DNA': 114} Link IDs: {'rna3p': 113} Time building chain proxies: 2.47, per 1000 atoms: 0.24 Number of scatterers: 10261 At special positions: 0 Unit cell: (113.42, 122.96, 109.18, 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 228 15.00 O 2361 8.00 N 1932 7.00 C 5726 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: 0.97 Conformation dependent library (CDL) restraints added in 239.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1316 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 73.0% alpha, 3.1% beta 114 base pairs and 211 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.505A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.736A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.894A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.375A 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 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.638A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.887A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 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: 4.486A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.551A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.580A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.916A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.046A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.939A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.051A 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 78 389 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 296 hydrogen bonds 592 hydrogen bond angles 0 basepair planarities 114 basepair parallelities 211 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1361 1.32 - 1.44: 3911 1.44 - 1.57: 5143 1.57 - 1.69: 456 1.69 - 1.81: 24 Bond restraints: 10895 Sorted by residual: bond pdb=" C ILE B 26 " pdb=" O ILE B 26 " ideal model delta sigma weight residual 1.237 1.197 0.040 1.23e-02 6.61e+03 1.07e+01 bond pdb=" C ASN D 67 " pdb=" O ASN D 67 " ideal model delta sigma weight residual 1.236 1.201 0.035 1.15e-02 7.56e+03 9.51e+00 bond pdb=" CZ ARG G 29 " pdb=" NH2 ARG G 29 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.40e+00 bond pdb=" CA ARG G 81 " pdb=" CB ARG G 81 " ideal model delta sigma weight residual 1.528 1.576 -0.047 1.56e-02 4.11e+03 9.16e+00 bond pdb=" CZ ARG C 29 " pdb=" NH2 ARG C 29 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.07e+00 ... (remaining 10890 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 14251 1.64 - 3.28: 1128 3.28 - 4.93: 248 4.93 - 6.57: 40 6.57 - 8.21: 8 Bond angle restraints: 15675 Sorted by residual: angle pdb=" CA HIS D 82 " pdb=" CB HIS D 82 " pdb=" CG HIS D 82 " ideal model delta sigma weight residual 113.80 109.84 3.96 1.00e+00 1.00e+00 1.57e+01 angle pdb=" O3' DA I -13 " pdb=" C3' DA I -13 " pdb=" C2' DA I -13 " ideal model delta sigma weight residual 111.50 117.43 -5.93 1.50e+00 4.44e-01 1.56e+01 angle pdb=" C4' DG I -55 " pdb=" C3' DG I -55 " pdb=" O3' DG I -55 " ideal model delta sigma weight residual 110.00 115.89 -5.89 1.50e+00 4.44e-01 1.54e+01 angle pdb=" OE1 GLN E 85 " pdb=" CD GLN E 85 " pdb=" NE2 GLN E 85 " ideal model delta sigma weight residual 122.60 118.69 3.91 1.00e+00 1.00e+00 1.53e+01 angle pdb=" C4' DT I -17 " pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " ideal model delta sigma weight residual 110.00 104.14 5.86 1.50e+00 4.44e-01 1.52e+01 ... (remaining 15670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.78: 4002 19.78 - 39.55: 945 39.55 - 59.33: 953 59.33 - 79.11: 56 79.11 - 98.88: 7 Dihedral angle restraints: 5963 sinusoidal: 3921 harmonic: 2042 Sorted by residual: dihedral pdb=" CA LEU E 61 " pdb=" C LEU E 61 " pdb=" N ILE E 62 " pdb=" CA ILE E 62 " ideal model delta harmonic sigma weight residual 180.00 151.54 28.46 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA LEU A 61 " pdb=" C LEU A 61 " pdb=" N ILE A 62 " pdb=" CA ILE A 62 " ideal model delta harmonic sigma weight residual 180.00 153.36 26.64 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA VAL G 107 " pdb=" C VAL G 107 " pdb=" N LEU G 108 " pdb=" CA LEU G 108 " ideal model delta harmonic sigma weight residual 180.00 -154.21 -25.79 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 5960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1534 0.062 - 0.124: 209 0.124 - 0.186: 35 0.186 - 0.248: 9 0.248 - 0.310: 2 Chirality restraints: 1789 Sorted by residual: chirality pdb=" CA ARG B 40 " pdb=" N ARG B 40 " pdb=" C ARG B 40 " pdb=" CB ARG B 40 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CA LYS C 36 " pdb=" N LYS C 36 " pdb=" C LYS C 36 " pdb=" CB LYS C 36 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA GLU H 71 " pdb=" N GLU H 71 " pdb=" C GLU H 71 " pdb=" CB GLU H 71 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1786 not shown) Planarity restraints: 1195 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I -7 " -0.099 2.00e-02 2.50e+03 6.11e-02 1.12e+02 pdb=" N9 DG I -7 " -0.020 2.00e-02 2.50e+03 pdb=" C8 DG I -7 " 0.117 2.00e-02 2.50e+03 pdb=" N7 DG I -7 " 0.077 2.00e-02 2.50e+03 pdb=" C5 DG I -7 " -0.024 2.00e-02 2.50e+03 pdb=" C6 DG I -7 " -0.037 2.00e-02 2.50e+03 pdb=" O6 DG I -7 " -0.076 2.00e-02 2.50e+03 pdb=" N1 DG I -7 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DG I -7 " 0.015 2.00e-02 2.50e+03 pdb=" N2 DG I -7 " 0.080 2.00e-02 2.50e+03 pdb=" N3 DG I -7 " -0.008 2.00e-02 2.50e+03 pdb=" C4 DG I -7 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -11 " 0.089 2.00e-02 2.50e+03 5.96e-02 1.07e+02 pdb=" N9 DG I -11 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DG I -11 " -0.105 2.00e-02 2.50e+03 pdb=" N7 DG I -11 " -0.085 2.00e-02 2.50e+03 pdb=" C5 DG I -11 " 0.013 2.00e-02 2.50e+03 pdb=" C6 DG I -11 " 0.040 2.00e-02 2.50e+03 pdb=" O6 DG I -11 " 0.069 2.00e-02 2.50e+03 pdb=" N1 DG I -11 " 0.017 2.00e-02 2.50e+03 pdb=" C2 DG I -11 " -0.020 2.00e-02 2.50e+03 pdb=" N2 DG I -11 " -0.087 2.00e-02 2.50e+03 pdb=" N3 DG I -11 " 0.014 2.00e-02 2.50e+03 pdb=" C4 DG I -11 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -13 " 0.111 2.00e-02 2.50e+03 5.95e-02 9.75e+01 pdb=" N9 DA I -13 " 0.008 2.00e-02 2.50e+03 pdb=" C8 DA I -13 " -0.102 2.00e-02 2.50e+03 pdb=" N7 DA I -13 " -0.050 2.00e-02 2.50e+03 pdb=" C5 DA I -13 " 0.022 2.00e-02 2.50e+03 pdb=" C6 DA I -13 " 0.027 2.00e-02 2.50e+03 pdb=" N6 DA I -13 " 0.087 2.00e-02 2.50e+03 pdb=" N1 DA I -13 " -0.026 2.00e-02 2.50e+03 pdb=" C2 DA I -13 " -0.055 2.00e-02 2.50e+03 pdb=" N3 DA I -13 " -0.032 2.00e-02 2.50e+03 pdb=" C4 DA I -13 " 0.010 2.00e-02 2.50e+03 ... (remaining 1192 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 3137 2.87 - 3.38: 8636 3.38 - 3.89: 20259 3.89 - 4.39: 23298 4.39 - 4.90: 32409 Nonbonded interactions: 87739 Sorted by model distance: nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 2.369 3.040 nonbonded pdb=" OD2 ASP E 106 " pdb=" NE ARG E 131 " model vdw 2.423 3.120 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.427 3.040 nonbonded pdb=" NH1 ARG A 72 " pdb=" OP1 DC I -23 " model vdw 2.440 3.120 nonbonded pdb=" O ALA D 124 " pdb=" OXT LYS D 125 " model vdw 2.446 3.040 ... (remaining 87734 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 58 through 135) } ncs_group { reference = (chain 'B' and resid 22 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 10 through 108) } ncs_group { reference = (chain 'D' and resid 32 through 125) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.840 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 10895 Z= 0.380 Angle : 0.994 8.212 15675 Z= 0.636 Chirality : 0.048 0.310 1789 Planarity : 0.014 0.125 1195 Dihedral : 27.854 98.881 4647 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 14.78 % Favored : 85.22 % 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 aren not related in a simple way. whole: 1.55 (0.30), residues: 692 helix: 1.85 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -1.32 (0.36), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG E 131 TYR 0.068 0.005 TYR H 42 PHE 0.054 0.004 PHE H 70 HIS 0.012 0.002 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00694 (10895) covalent geometry : angle 0.99360 (15675) hydrogen bonds : bond 0.11763 ( 685) hydrogen bonds : angle 3.94742 ( 1744) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.262 Fit side-chains REVERT: C 75 LYS cc_start: 0.8227 (mttp) cc_final: 0.7490 (tptt) REVERT: C 95 LYS cc_start: 0.8838 (tttt) cc_final: 0.8233 (ttpt) REVERT: E 94 GLU cc_start: 0.8407 (tp30) cc_final: 0.8166 (mm-30) REVERT: F 39 ARG cc_start: 0.8046 (mpt180) cc_final: 0.7800 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 1.0685 time to fit residues: 155.7498 Evaluate side-chains 126 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 0.0870 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 104 GLN D 82 HIS D 84 ASN E 76 GLN G 24 GLN H 63 ASN H 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.152831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.118427 restraints weight = 11214.969| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.26 r_work: 0.3277 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10895 Z= 0.148 Angle : 0.539 5.239 15675 Z= 0.332 Chirality : 0.033 0.144 1789 Planarity : 0.004 0.039 1195 Dihedral : 29.732 101.236 3267 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 2.23 % Allowed : 15.98 % Favored : 81.79 % 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 aren not related in a simple way. whole: 2.82 (0.31), residues: 692 helix: 2.81 (0.22), residues: 514 sheet: None (None), residues: 0 loop : -1.12 (0.38), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 72 TYR 0.008 0.001 TYR F 51 PHE 0.007 0.001 PHE B 61 HIS 0.002 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00310 (10895) covalent geometry : angle 0.53875 (15675) hydrogen bonds : bond 0.04100 ( 685) hydrogen bonds : angle 2.86822 ( 1744) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8323 (tt0) cc_final: 0.7937 (tt0) REVERT: B 25 ASN cc_start: 0.7926 (m-40) cc_final: 0.7653 (m-40) REVERT: B 35 ARG cc_start: 0.8728 (mtp85) cc_final: 0.8465 (mtp180) REVERT: C 75 LYS cc_start: 0.8071 (mttp) cc_final: 0.7309 (tptt) REVERT: E 94 GLU cc_start: 0.8338 (tp30) cc_final: 0.8061 (mm-30) REVERT: H 108 LYS cc_start: 0.8217 (mmtt) cc_final: 0.7944 (mmtm) REVERT: H 113 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8238 (mm-30) outliers start: 13 outliers final: 4 residues processed: 135 average time/residue: 1.0467 time to fit residues: 147.2623 Evaluate side-chains 131 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 15 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 74 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 82 HIS D 84 ASN E 76 GLN G 104 GLN H 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.150750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.115884 restraints weight = 11296.996| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.27 r_work: 0.3228 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10895 Z= 0.167 Angle : 0.535 4.994 15675 Z= 0.330 Chirality : 0.034 0.126 1789 Planarity : 0.004 0.036 1195 Dihedral : 29.795 96.474 3267 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.06 % Allowed : 16.32 % Favored : 81.62 % 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 aren not related in a simple way. whole: 3.04 (0.31), residues: 692 helix: 3.01 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.17 (0.38), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 72 TYR 0.009 0.001 TYR B 51 PHE 0.008 0.001 PHE B 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00363 (10895) covalent geometry : angle 0.53540 (15675) hydrogen bonds : bond 0.04418 ( 685) hydrogen bonds : angle 2.81562 ( 1744) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.302 Fit side-chains REVERT: A 133 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8502 (mt-10) REVERT: B 25 ASN cc_start: 0.8162 (m-40) cc_final: 0.7962 (m-40) REVERT: B 93 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.8018 (mm-40) REVERT: C 75 LYS cc_start: 0.8095 (mttp) cc_final: 0.7368 (tptt) REVERT: C 95 LYS cc_start: 0.8686 (tttt) cc_final: 0.8446 (tttp) REVERT: D 85 LYS cc_start: 0.9077 (mmtp) cc_final: 0.8862 (mptt) REVERT: H 108 LYS cc_start: 0.8200 (mmtt) cc_final: 0.7923 (mmtm) outliers start: 12 outliers final: 5 residues processed: 133 average time/residue: 1.0171 time to fit residues: 140.8164 Evaluate side-chains 130 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 82 HIS E 76 GLN G 104 GLN H 63 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.144781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.109022 restraints weight = 11374.399| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.30 r_work: 0.3165 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 10895 Z= 0.269 Angle : 0.603 5.645 15675 Z= 0.362 Chirality : 0.038 0.139 1789 Planarity : 0.005 0.039 1195 Dihedral : 30.204 91.521 3267 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.41 % Allowed : 16.49 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.55 (0.31), residues: 692 helix: 2.66 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.42 (0.36), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 72 TYR 0.009 0.002 TYR F 51 PHE 0.008 0.002 PHE B 61 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00619 (10895) covalent geometry : angle 0.60304 (15675) hydrogen bonds : bond 0.05883 ( 685) hydrogen bonds : angle 2.98089 ( 1744) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8417 (mt-10) REVERT: B 93 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8069 (mm-40) REVERT: C 75 LYS cc_start: 0.8106 (mttp) cc_final: 0.7388 (tptt) REVERT: D 85 LYS cc_start: 0.9134 (mmtp) cc_final: 0.8930 (mptt) REVERT: G 75 LYS cc_start: 0.8071 (mmmt) cc_final: 0.7185 (tptt) outliers start: 14 outliers final: 6 residues processed: 136 average time/residue: 0.9794 time to fit residues: 138.8000 Evaluate side-chains 131 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 4 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 104 GLN D 82 HIS E 76 GLN G 104 GLN H 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.145646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.110310 restraints weight = 11306.675| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.26 r_work: 0.3176 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10895 Z= 0.211 Angle : 0.581 5.463 15675 Z= 0.352 Chirality : 0.036 0.135 1789 Planarity : 0.004 0.038 1195 Dihedral : 30.196 92.251 3267 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.92 % Allowed : 16.32 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.63 (0.31), residues: 692 helix: 2.73 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.43 (0.36), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 35 TYR 0.009 0.002 TYR F 51 PHE 0.008 0.002 PHE B 61 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00474 (10895) covalent geometry : angle 0.58051 (15675) hydrogen bonds : bond 0.05472 ( 685) hydrogen bonds : angle 2.96690 ( 1744) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8505 (mt-10) REVERT: B 29 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7460 (mm) REVERT: B 93 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8029 (mm-40) REVERT: C 75 LYS cc_start: 0.8069 (mttp) cc_final: 0.7353 (tptt) REVERT: D 85 LYS cc_start: 0.9132 (mmtp) cc_final: 0.8932 (mptt) REVERT: E 94 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8136 (mm-30) REVERT: E 133 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8403 (mt-10) REVERT: G 75 LYS cc_start: 0.8137 (mmmt) cc_final: 0.7208 (tptt) REVERT: H 71 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7996 (mt-10) outliers start: 17 outliers final: 6 residues processed: 131 average time/residue: 0.9984 time to fit residues: 136.4115 Evaluate side-chains 130 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 76 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 104 GLN D 82 HIS E 76 GLN G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.142948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.107143 restraints weight = 11713.591| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.29 r_work: 0.3134 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10895 Z= 0.274 Angle : 0.612 5.633 15675 Z= 0.367 Chirality : 0.039 0.138 1789 Planarity : 0.005 0.043 1195 Dihedral : 30.267 92.589 3267 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.23 % Allowed : 16.84 % Favored : 80.93 % 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 aren not related in a simple way. whole: 2.32 (0.30), residues: 692 helix: 2.51 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.57 (0.36), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 35 TYR 0.009 0.002 TYR H 121 PHE 0.008 0.002 PHE B 61 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00632 (10895) covalent geometry : angle 0.61175 (15675) hydrogen bonds : bond 0.05943 ( 685) hydrogen bonds : angle 2.99011 ( 1744) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.294 Fit side-chains REVERT: A 133 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8410 (mt-10) REVERT: B 25 ASN cc_start: 0.8255 (m-40) cc_final: 0.8008 (m110) REVERT: B 29 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7330 (mm) REVERT: B 77 LYS cc_start: 0.8909 (mptp) cc_final: 0.8660 (mptp) REVERT: B 93 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8051 (mm-40) REVERT: C 75 LYS cc_start: 0.8088 (mttp) cc_final: 0.7238 (tptt) REVERT: D 85 LYS cc_start: 0.9123 (mmtp) cc_final: 0.8914 (mptt) REVERT: D 108 LYS cc_start: 0.8323 (mtpp) cc_final: 0.7859 (mmtp) REVERT: E 94 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8192 (mm-30) REVERT: E 133 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8430 (mt-10) REVERT: F 24 ASP cc_start: 0.7268 (t0) cc_final: 0.6824 (t70) REVERT: G 75 LYS cc_start: 0.7965 (mmmt) cc_final: 0.7139 (tptt) outliers start: 13 outliers final: 6 residues processed: 136 average time/residue: 0.9921 time to fit residues: 140.7448 Evaluate side-chains 133 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 82 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN F 27 GLN G 104 GLN H 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.144432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.108844 restraints weight = 11517.966| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.28 r_work: 0.3156 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10895 Z= 0.175 Angle : 0.578 5.836 15675 Z= 0.351 Chirality : 0.035 0.135 1789 Planarity : 0.004 0.039 1195 Dihedral : 30.250 93.844 3267 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.55 % Allowed : 17.70 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.66 (0.31), residues: 692 helix: 2.78 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.50 (0.36), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 35 TYR 0.010 0.001 TYR F 51 PHE 0.008 0.001 PHE B 61 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00380 (10895) covalent geometry : angle 0.57757 (15675) hydrogen bonds : bond 0.05171 ( 685) hydrogen bonds : angle 2.95440 ( 1744) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.285 Fit side-chains REVERT: A 133 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8475 (mt-10) REVERT: B 35 ARG cc_start: 0.8743 (mtp85) cc_final: 0.8445 (mtp180) REVERT: B 93 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8013 (mm-40) REVERT: D 85 LYS cc_start: 0.9108 (mmtp) cc_final: 0.8898 (mptt) REVERT: D 108 LYS cc_start: 0.8334 (mtpp) cc_final: 0.7852 (mmtp) REVERT: E 94 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8170 (mm-30) REVERT: F 24 ASP cc_start: 0.7217 (t0) cc_final: 0.6822 (t70) REVERT: G 75 LYS cc_start: 0.7937 (mmmt) cc_final: 0.7117 (tptt) outliers start: 9 outliers final: 5 residues processed: 129 average time/residue: 0.9820 time to fit residues: 132.0783 Evaluate side-chains 127 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 4 optimal weight: 0.1980 chunk 54 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 0.0010 chunk 34 optimal weight: 0.8980 chunk 59 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 104 GLN D 82 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN F 27 GLN G 104 GLN H 63 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.145323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.109812 restraints weight = 11551.670| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.28 r_work: 0.3170 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10895 Z= 0.159 Angle : 0.573 6.255 15675 Z= 0.347 Chirality : 0.034 0.131 1789 Planarity : 0.004 0.038 1195 Dihedral : 30.195 95.274 3267 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.72 % Allowed : 18.21 % Favored : 80.07 % 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 aren not related in a simple way. whole: 2.83 (0.31), residues: 692 helix: 2.88 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.40 (0.37), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 79 TYR 0.009 0.001 TYR F 51 PHE 0.008 0.001 PHE D 65 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00344 (10895) covalent geometry : angle 0.57285 (15675) hydrogen bonds : bond 0.04757 ( 685) hydrogen bonds : angle 2.90321 ( 1744) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.291 Fit side-chains REVERT: A 133 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8472 (mt-10) REVERT: B 25 ASN cc_start: 0.8141 (m-40) cc_final: 0.7876 (m-40) REVERT: B 35 ARG cc_start: 0.8730 (mtp85) cc_final: 0.8421 (mtp180) REVERT: B 93 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7994 (mm-40) REVERT: C 75 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7488 (mtpp) REVERT: D 85 LYS cc_start: 0.9106 (mmtp) cc_final: 0.8898 (mptt) REVERT: E 94 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8128 (mm-30) REVERT: E 133 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8430 (mt-10) REVERT: F 24 ASP cc_start: 0.7212 (t0) cc_final: 0.6818 (t70) REVERT: G 75 LYS cc_start: 0.7991 (mmmt) cc_final: 0.7134 (tptt) outliers start: 10 outliers final: 6 residues processed: 130 average time/residue: 0.9913 time to fit residues: 134.2975 Evaluate side-chains 130 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 15 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 46 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 88 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 82 HIS E 76 GLN F 25 ASN F 27 GLN G 104 GLN H 63 ASN H 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.145494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.109954 restraints weight = 11554.814| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.28 r_work: 0.3169 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10895 Z= 0.177 Angle : 0.561 6.698 15675 Z= 0.341 Chirality : 0.034 0.132 1789 Planarity : 0.004 0.042 1195 Dihedral : 30.020 97.071 3267 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.06 % Allowed : 17.87 % Favored : 80.07 % 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 aren not related in a simple way. whole: 2.85 (0.31), residues: 692 helix: 2.89 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.29 (0.37), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 35 TYR 0.009 0.001 TYR B 51 PHE 0.008 0.001 PHE B 61 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00392 (10895) covalent geometry : angle 0.56142 (15675) hydrogen bonds : bond 0.04702 ( 685) hydrogen bonds : angle 2.84143 ( 1744) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.285 Fit side-chains REVERT: A 73 GLU cc_start: 0.8350 (tt0) cc_final: 0.7898 (tt0) REVERT: A 133 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8547 (mt-10) REVERT: B 25 ASN cc_start: 0.8191 (m-40) cc_final: 0.7961 (m110) REVERT: B 35 ARG cc_start: 0.8723 (mtp85) cc_final: 0.8404 (mtp180) REVERT: B 93 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7960 (mm-40) REVERT: D 85 LYS cc_start: 0.9087 (mmtp) cc_final: 0.8879 (mptt) REVERT: D 108 LYS cc_start: 0.8252 (mtpp) cc_final: 0.7732 (mmtp) REVERT: E 94 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8101 (mm-30) REVERT: E 133 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8388 (mt-10) REVERT: F 24 ASP cc_start: 0.7162 (t0) cc_final: 0.6748 (t70) REVERT: G 75 LYS cc_start: 0.7938 (mmmt) cc_final: 0.7111 (tptt) REVERT: H 71 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7872 (mt-10) outliers start: 12 outliers final: 5 residues processed: 132 average time/residue: 1.0513 time to fit residues: 144.5647 Evaluate side-chains 127 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 15 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 24 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 82 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN F 27 GLN G 104 GLN H 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.145124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109652 restraints weight = 11472.874| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.28 r_work: 0.3170 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10895 Z= 0.193 Angle : 0.564 6.790 15675 Z= 0.342 Chirality : 0.035 0.133 1789 Planarity : 0.005 0.050 1195 Dihedral : 29.954 95.284 3267 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.23 % Allowed : 18.04 % Favored : 79.73 % 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 aren not related in a simple way. whole: 2.80 (0.31), residues: 692 helix: 2.85 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.30 (0.36), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 35 TYR 0.010 0.001 TYR B 51 PHE 0.008 0.002 PHE B 61 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00433 (10895) covalent geometry : angle 0.56402 (15675) hydrogen bonds : bond 0.04916 ( 685) hydrogen bonds : angle 2.84586 ( 1744) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.293 Fit side-chains REVERT: A 133 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8483 (mt-10) REVERT: B 25 ASN cc_start: 0.8201 (m-40) cc_final: 0.7900 (m110) REVERT: B 77 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8482 (mptp) REVERT: B 93 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7934 (mm-40) REVERT: C 75 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7252 (mtpp) REVERT: C 95 LYS cc_start: 0.8525 (tttt) cc_final: 0.8246 (tttp) REVERT: D 85 LYS cc_start: 0.9095 (mmtp) cc_final: 0.8890 (mptt) REVERT: E 94 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8158 (mm-30) REVERT: E 133 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8393 (mt-10) REVERT: F 24 ASP cc_start: 0.7150 (t0) cc_final: 0.6761 (t70) REVERT: G 75 LYS cc_start: 0.7939 (mmmt) cc_final: 0.7104 (tptt) REVERT: H 71 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7884 (mt-10) outliers start: 13 outliers final: 6 residues processed: 129 average time/residue: 1.0515 time to fit residues: 141.2968 Evaluate side-chains 132 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 22 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 82 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN F 27 GLN G 104 GLN H 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.145542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110054 restraints weight = 11551.898| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.28 r_work: 0.3172 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10895 Z= 0.171 Angle : 0.564 6.586 15675 Z= 0.342 Chirality : 0.034 0.132 1789 Planarity : 0.004 0.044 1195 Dihedral : 29.952 95.392 3267 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.06 % Allowed : 18.38 % Favored : 79.55 % 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 aren not related in a simple way. whole: 2.84 (0.31), residues: 692 helix: 2.87 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.30 (0.37), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 72 TYR 0.009 0.001 TYR B 51 PHE 0.008 0.001 PHE B 61 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00375 (10895) covalent geometry : angle 0.56359 (15675) hydrogen bonds : bond 0.04749 ( 685) hydrogen bonds : angle 2.84011 ( 1744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4616.30 seconds wall clock time: 78 minutes 58.76 seconds (4738.76 seconds total)