Starting phenix.real_space_refine on Mon Jul 28 03:28:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ybk_39120/07_2025/8ybk_39120.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ybk_39120/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ybk_39120/07_2025/8ybk_39120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ybk_39120/07_2025/8ybk_39120.map" model { file = "/net/cci-nas-00/data/ceres_data/8ybk_39120/07_2025/8ybk_39120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ybk_39120/07_2025/8ybk_39120.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.29, per 1000 atoms: 0.61 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: 2.70 Conformation dependent library (CDL) restraints added in 674.7 milliseconds 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: 5.16 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: 3.74 Time building geometry restraints manager: 3.17 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 29.360 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 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:13.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.480 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.012 0.002 HIS D 82 PHE 0.054 0.004 PHE H 70 TYR 0.068 0.005 TYR H 42 ARG 0.017 0.002 ARG E 131 Details of bonding type rmsd hydrogen bonds : bond 0.11763 ( 685) hydrogen bonds : angle 3.94742 ( 1744) covalent geometry : bond 0.00694 (10895) covalent geometry : angle 0.99360 (15675) *********************** 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 : 0.793 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: 2.0047 time to fit residues: 293.0269 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 : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 26 optimal weight: 0.1980 chunk 42 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.150921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.116242 restraints weight = 11169.312| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.26 r_work: 0.3233 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10895 Z= 0.162 Angle : 0.548 5.245 15675 Z= 0.337 Chirality : 0.034 0.144 1789 Planarity : 0.004 0.039 1195 Dihedral : 29.873 100.565 3267 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 1.89 % Allowed : 16.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.31), residues: 692 helix: 2.77 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.29 (0.37), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE B 61 TYR 0.009 0.001 TYR F 51 ARG 0.008 0.001 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.04451 ( 685) hydrogen bonds : angle 2.89947 ( 1744) covalent geometry : bond 0.00347 (10895) covalent geometry : angle 0.54832 (15675) *********************** 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 139 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8316 (tt0) cc_final: 0.7930 (tt0) REVERT: B 25 ASN cc_start: 0.8013 (m-40) cc_final: 0.7714 (m-40) REVERT: B 35 ARG cc_start: 0.8744 (mtp85) cc_final: 0.8442 (mtp180) REVERT: C 75 LYS cc_start: 0.8043 (mttp) cc_final: 0.7294 (tptt) REVERT: E 94 GLU cc_start: 0.8376 (tp30) cc_final: 0.8152 (mm-30) REVERT: H 108 LYS cc_start: 0.8276 (mmtt) cc_final: 0.8056 (mmtm) REVERT: H 113 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8290 (mm-30) outliers start: 11 outliers final: 4 residues processed: 133 average time/residue: 1.9239 time to fit residues: 268.2089 Evaluate side-chains 129 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 125 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 51 optimal weight: 0.0020 chunk 75 optimal weight: 4.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- 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 H 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.149262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114270 restraints weight = 11232.091| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.26 r_work: 0.3215 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10895 Z= 0.184 Angle : 0.551 5.099 15675 Z= 0.337 Chirality : 0.035 0.130 1789 Planarity : 0.004 0.044 1195 Dihedral : 29.930 96.473 3267 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.31), residues: 692 helix: 2.86 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.28 (0.37), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE B 61 TYR 0.009 0.001 TYR B 51 ARG 0.009 0.001 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.04804 ( 685) hydrogen bonds : angle 2.86456 ( 1744) covalent geometry : bond 0.00408 (10895) covalent geometry : angle 0.55081 (15675) *********************** 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 142 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.942 Fit side-chains REVERT: A 133 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8532 (mt-10) REVERT: B 35 ARG cc_start: 0.8754 (mtp85) cc_final: 0.8495 (mtp180) REVERT: C 75 LYS cc_start: 0.8107 (mttp) cc_final: 0.7372 (tptt) REVERT: D 85 LYS cc_start: 0.9088 (mmtp) cc_final: 0.8874 (mptt) REVERT: E 94 GLU cc_start: 0.8429 (tp30) cc_final: 0.8185 (mm-30) REVERT: G 75 LYS cc_start: 0.7996 (mmmt) cc_final: 0.7052 (tptt) REVERT: H 108 LYS cc_start: 0.8266 (mmtt) cc_final: 0.7981 (mmtm) outliers start: 13 outliers final: 7 residues processed: 136 average time/residue: 2.4026 time to fit residues: 341.9913 Evaluate side-chains 132 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS 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 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 46 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 39 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.149724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.114764 restraints weight = 11199.711| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.25 r_work: 0.3217 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10895 Z= 0.166 Angle : 0.548 5.539 15675 Z= 0.336 Chirality : 0.034 0.129 1789 Planarity : 0.004 0.054 1195 Dihedral : 29.918 96.721 3267 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.23 % Allowed : 17.35 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.31), residues: 692 helix: 2.97 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.21 (0.37), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE B 61 TYR 0.009 0.001 TYR B 51 ARG 0.004 0.000 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.04594 ( 685) hydrogen bonds : angle 2.85024 ( 1744) covalent geometry : bond 0.00360 (10895) covalent geometry : angle 0.54816 (15675) *********************** 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 135 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.801 Fit side-chains REVERT: A 133 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8527 (mt-10) REVERT: B 35 ARG cc_start: 0.8751 (mtp85) cc_final: 0.8489 (mtp180) REVERT: C 75 LYS cc_start: 0.8109 (mttp) cc_final: 0.7374 (tptt) REVERT: D 85 LYS cc_start: 0.9089 (mmtp) cc_final: 0.8876 (mptt) REVERT: E 94 GLU cc_start: 0.8414 (tp30) cc_final: 0.8199 (mm-30) REVERT: G 73 ASN cc_start: 0.7682 (t0) cc_final: 0.7444 (t0) REVERT: G 75 LYS cc_start: 0.7928 (mmmt) cc_final: 0.7135 (tmtt) REVERT: H 71 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8004 (mt-10) REVERT: H 108 LYS cc_start: 0.8264 (mmtt) cc_final: 0.7982 (mmtm) outliers start: 13 outliers final: 4 residues processed: 127 average time/residue: 1.9677 time to fit residues: 261.3682 Evaluate side-chains 128 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU 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 Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 32 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.149984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.115105 restraints weight = 11165.169| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.26 r_work: 0.3223 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 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 : 0.004 0.031 10895 Z= 0.163 Angle : 0.540 5.208 15675 Z= 0.332 Chirality : 0.034 0.128 1789 Planarity : 0.004 0.038 1195 Dihedral : 29.893 97.106 3267 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.58 % Allowed : 16.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.31), residues: 692 helix: 3.00 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.17 (0.37), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE B 61 TYR 0.009 0.001 TYR B 51 ARG 0.004 0.000 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.04486 ( 685) hydrogen bonds : angle 2.82421 ( 1744) covalent geometry : bond 0.00353 (10895) covalent geometry : angle 0.54005 (15675) *********************** 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 137 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.809 Fit side-chains REVERT: A 133 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8529 (mt-10) REVERT: B 93 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7815 (mt0) REVERT: C 75 LYS cc_start: 0.8111 (mttp) cc_final: 0.7419 (tptt) REVERT: D 85 LYS cc_start: 0.9082 (mmtp) cc_final: 0.8872 (mptt) REVERT: E 94 GLU cc_start: 0.8408 (tp30) cc_final: 0.8201 (mm-30) REVERT: E 133 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8338 (mt-10) REVERT: G 73 ASN cc_start: 0.7654 (t0) cc_final: 0.7388 (t0) REVERT: G 75 LYS cc_start: 0.7947 (mmmt) cc_final: 0.7170 (tmtt) REVERT: H 71 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7998 (mt-10) REVERT: H 108 LYS cc_start: 0.8258 (mmtt) cc_final: 0.7978 (mmtm) outliers start: 15 outliers final: 5 residues processed: 129 average time/residue: 1.9447 time to fit residues: 262.5709 Evaluate side-chains 130 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.148206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113254 restraints weight = 11164.274| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.26 r_work: 0.3190 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10895 Z= 0.208 Angle : 0.564 5.577 15675 Z= 0.343 Chirality : 0.036 0.133 1789 Planarity : 0.005 0.059 1195 Dihedral : 29.967 94.376 3267 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.41 % Allowed : 16.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.31), residues: 692 helix: 2.85 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.29 (0.37), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.008 0.002 PHE B 61 TYR 0.010 0.002 TYR B 51 ARG 0.010 0.001 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.05130 ( 685) hydrogen bonds : angle 2.85433 ( 1744) covalent geometry : bond 0.00470 (10895) covalent geometry : angle 0.56353 (15675) *********************** 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 139 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.856 Fit side-chains REVERT: A 133 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8484 (mt-10) REVERT: B 35 ARG cc_start: 0.8790 (mtp85) cc_final: 0.8456 (mtp180) REVERT: C 75 LYS cc_start: 0.8115 (mttp) cc_final: 0.7408 (tptt) REVERT: C 95 LYS cc_start: 0.8629 (tttt) cc_final: 0.8360 (tttm) REVERT: D 85 LYS cc_start: 0.9053 (mmtp) cc_final: 0.8852 (mptt) REVERT: E 133 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8378 (mt-10) REVERT: G 73 ASN cc_start: 0.7738 (t0) cc_final: 0.7522 (t0) REVERT: G 75 LYS cc_start: 0.7930 (mmmt) cc_final: 0.7095 (tptt) REVERT: H 108 LYS cc_start: 0.8315 (mmtt) cc_final: 0.8040 (mmtm) outliers start: 14 outliers final: 5 residues processed: 133 average time/residue: 1.9724 time to fit residues: 274.5702 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 : 0.773 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 G 104 GLN H 47 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 = 0.3845 r_free = 0.3845 target = 0.146785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.111399 restraints weight = 11387.672| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.30 r_work: 0.3187 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10895 Z= 0.199 Angle : 0.561 5.392 15675 Z= 0.341 Chirality : 0.035 0.134 1789 Planarity : 0.004 0.047 1195 Dihedral : 29.966 94.497 3267 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.55 % Allowed : 18.21 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.31), residues: 692 helix: 2.86 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.29 (0.37), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE B 61 TYR 0.010 0.001 TYR B 51 ARG 0.009 0.000 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.05031 ( 685) hydrogen bonds : angle 2.85808 ( 1744) covalent geometry : bond 0.00448 (10895) covalent geometry : angle 0.56068 (15675) *********************** 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 : 0.768 Fit side-chains REVERT: A 73 GLU cc_start: 0.8416 (tt0) cc_final: 0.7788 (tt0) REVERT: A 133 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8487 (mt-10) REVERT: B 29 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7429 (mm) REVERT: C 75 LYS cc_start: 0.8100 (mttp) cc_final: 0.7387 (tptt) REVERT: D 85 LYS cc_start: 0.9044 (mmtp) cc_final: 0.8838 (mptt) REVERT: E 133 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8383 (mt-10) REVERT: G 73 ASN cc_start: 0.7723 (t0) cc_final: 0.7474 (t0) REVERT: G 75 LYS cc_start: 0.7885 (mmmt) cc_final: 0.7044 (tptt) REVERT: H 108 LYS cc_start: 0.8286 (mmtt) cc_final: 0.8009 (mmtm) outliers start: 9 outliers final: 5 residues processed: 128 average time/residue: 1.9242 time to fit residues: 257.9411 Evaluate side-chains 130 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 G 104 GLN H 47 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 = 0.3851 r_free = 0.3851 target = 0.147374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.112092 restraints weight = 11304.872| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.29 r_work: 0.3200 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10895 Z= 0.171 Angle : 0.555 6.723 15675 Z= 0.338 Chirality : 0.034 0.132 1789 Planarity : 0.004 0.055 1195 Dihedral : 29.961 94.744 3267 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.89 % Allowed : 18.21 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.31), residues: 692 helix: 2.94 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.27 (0.37), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE B 61 TYR 0.010 0.001 TYR B 51 ARG 0.009 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.04802 ( 685) hydrogen bonds : angle 2.84570 ( 1744) covalent geometry : bond 0.00374 (10895) covalent geometry : angle 0.55547 (15675) *********************** 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 133 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.862 Fit side-chains REVERT: A 73 GLU cc_start: 0.8405 (tt0) cc_final: 0.7773 (tt0) REVERT: A 133 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8472 (mt-10) REVERT: B 93 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7795 (mt0) REVERT: C 75 LYS cc_start: 0.8065 (mttp) cc_final: 0.7340 (tptt) REVERT: D 85 LYS cc_start: 0.9035 (mmtp) cc_final: 0.8829 (mptt) REVERT: E 133 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8378 (mt-10) REVERT: G 75 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7047 (tptt) REVERT: H 108 LYS cc_start: 0.8250 (mmtt) cc_final: 0.7969 (mmtm) outliers start: 11 outliers final: 5 residues processed: 129 average time/residue: 2.0310 time to fit residues: 274.1222 Evaluate side-chains 129 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 67 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 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 = 0.3810 r_free = 0.3810 target = 0.144230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.108469 restraints weight = 11629.314| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.29 r_work: 0.3153 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10895 Z= 0.226 Angle : 0.579 5.621 15675 Z= 0.350 Chirality : 0.037 0.134 1789 Planarity : 0.005 0.063 1195 Dihedral : 30.069 92.867 3267 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.72 % Allowed : 18.38 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.31), residues: 692 helix: 2.77 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.36 (0.37), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.009 0.002 PHE B 61 TYR 0.009 0.002 TYR B 51 ARG 0.011 0.001 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.05390 ( 685) hydrogen bonds : angle 2.88917 ( 1744) covalent geometry : bond 0.00514 (10895) covalent geometry : angle 0.57888 (15675) *********************** 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 134 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8377 (tt0) cc_final: 0.7748 (tt0) REVERT: A 133 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8540 (mt-10) REVERT: B 29 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7319 (mm) REVERT: C 73 ASN cc_start: 0.8250 (t0) cc_final: 0.7471 (t0) REVERT: C 75 LYS cc_start: 0.8100 (mttp) cc_final: 0.7171 (tptt) REVERT: D 85 LYS cc_start: 0.9017 (mmtp) cc_final: 0.8810 (mptt) REVERT: D 108 LYS cc_start: 0.8330 (mtpp) cc_final: 0.7772 (mmtm) REVERT: E 133 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8411 (mt-10) REVERT: F 24 ASP cc_start: 0.7198 (t0) cc_final: 0.6789 (t70) REVERT: G 75 LYS cc_start: 0.7847 (mmmt) cc_final: 0.7005 (tptt) outliers start: 10 outliers final: 5 residues processed: 131 average time/residue: 2.4193 time to fit residues: 331.6772 Evaluate side-chains 130 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN G 104 GLN H 47 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 = 0.3817 r_free = 0.3817 target = 0.144765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109047 restraints weight = 11580.575| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.28 r_work: 0.3161 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1442 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= 0.186 Angle : 0.570 5.546 15675 Z= 0.345 Chirality : 0.035 0.134 1789 Planarity : 0.005 0.043 1195 Dihedral : 30.066 93.092 3267 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.37 % Allowed : 18.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.31), residues: 692 helix: 2.83 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.34 (0.37), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.008 0.002 PHE B 61 TYR 0.009 0.001 TYR F 51 ARG 0.010 0.001 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.05149 ( 685) hydrogen bonds : angle 2.87874 ( 1744) covalent geometry : bond 0.00409 (10895) covalent geometry : angle 0.56952 (15675) ********************** 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 131 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8496 (mt-10) REVERT: C 73 ASN cc_start: 0.8248 (t0) cc_final: 0.7468 (t0) REVERT: C 75 LYS cc_start: 0.8093 (mttp) cc_final: 0.7165 (tptt) REVERT: D 108 LYS cc_start: 0.8338 (mtpp) cc_final: 0.7813 (mmtm) REVERT: E 133 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8417 (mt-10) REVERT: F 24 ASP cc_start: 0.7187 (t0) cc_final: 0.6781 (t70) REVERT: G 75 LYS cc_start: 0.7857 (mmmt) cc_final: 0.7013 (tptt) outliers start: 8 outliers final: 5 residues processed: 128 average time/residue: 1.9317 time to fit residues: 258.8512 Evaluate side-chains 129 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3814 r_free = 0.3814 target = 0.144474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.108782 restraints weight = 11527.449| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.27 r_work: 0.3156 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10895 Z= 0.218 Angle : 0.577 6.628 15675 Z= 0.347 Chirality : 0.036 0.136 1789 Planarity : 0.005 0.042 1195 Dihedral : 30.032 94.049 3267 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.72 % Allowed : 18.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.31), residues: 692 helix: 2.78 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.37 (0.37), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.008 0.002 PHE B 61 TYR 0.009 0.002 TYR B 51 ARG 0.010 0.001 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.05223 ( 685) hydrogen bonds : angle 2.86447 ( 1744) covalent geometry : bond 0.00497 (10895) covalent geometry : angle 0.57677 (15675) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9224.67 seconds wall clock time: 161 minutes 59.83 seconds (9719.83 seconds total)