Starting phenix.real_space_refine on Wed Mar 4 06:06:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t79_10390/03_2026/6t79_10390.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t79_10390/03_2026/6t79_10390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6t79_10390/03_2026/6t79_10390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t79_10390/03_2026/6t79_10390.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t79_10390/03_2026/6t79_10390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t79_10390/03_2026/6t79_10390.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 290 5.49 5 S 10 5.16 5 C 6732 2.51 5 N 2270 2.21 5 O 2819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12121 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 809 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 678 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2959 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2986 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Time building chain proxies: 2.74, per 1000 atoms: 0.23 Number of scatterers: 12121 At special positions: 0 Unit cell: (84, 124.95, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 290 15.00 O 2819 8.00 N 2270 7.00 C 6732 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: 0.98 Conformation dependent library (CDL) restraints added in 503.9 milliseconds 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1450 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 68.9% alpha, 3.1% beta 142 base pairs and 264 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.601A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.632A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.654A pdb=" N ARG B 36 " --> pdb=" O PRO B 32 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.859A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.543A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.582A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.562A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.256A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.544A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 removed outlier: 3.686A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 53 through 81 removed outlier: 3.521A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.831A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.600A pdb=" N ALA E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.540A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 removed outlier: 3.600A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.976A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.732A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.582A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.563A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.254A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.546A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 removed outlier: 3.687A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 53 through 81 removed outlier: 3.522A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.830A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.497A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.526A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.021A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (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: 7.267A 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: 6.927A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (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 78 364 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 340 hydrogen bonds 680 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 264 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2040 1.33 - 1.45: 4244 1.45 - 1.56: 6042 1.56 - 1.68: 580 1.68 - 1.80: 20 Bond restraints: 12926 Sorted by residual: bond pdb=" C ALA C 47 " pdb=" N PRO C 48 " ideal model delta sigma weight residual 1.336 1.379 -0.043 1.23e-02 6.61e+03 1.22e+01 bond pdb=" C ALA G 47 " pdb=" N PRO G 48 " ideal model delta sigma weight residual 1.336 1.378 -0.043 1.23e-02 6.61e+03 1.22e+01 bond pdb=" C3' DC I 13 " pdb=" O3' DC I 13 " ideal model delta sigma weight residual 1.422 1.485 -0.063 3.00e-02 1.11e+03 4.36e+00 bond pdb=" C3' DT I 87 " pdb=" O3' DT I 87 " ideal model delta sigma weight residual 1.422 1.481 -0.059 3.00e-02 1.11e+03 3.81e+00 bond pdb=" C3' DG J 35 " pdb=" O3' DG J 35 " ideal model delta sigma weight residual 1.422 1.476 -0.054 3.00e-02 1.11e+03 3.24e+00 ... (remaining 12921 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 17607 1.73 - 3.46: 995 3.46 - 5.19: 69 5.19 - 6.91: 8 6.91 - 8.64: 8 Bond angle restraints: 18687 Sorted by residual: angle pdb=" CA GLU G 91 " pdb=" CB GLU G 91 " pdb=" CG GLU G 91 " ideal model delta sigma weight residual 114.10 122.74 -8.64 2.00e+00 2.50e-01 1.87e+01 angle pdb=" CA GLU C 91 " pdb=" CB GLU C 91 " pdb=" CG GLU C 91 " ideal model delta sigma weight residual 114.10 122.71 -8.61 2.00e+00 2.50e-01 1.85e+01 angle pdb=" CB GLU C 91 " pdb=" CG GLU C 91 " pdb=" CD GLU C 91 " ideal model delta sigma weight residual 112.60 119.72 -7.12 1.70e+00 3.46e-01 1.76e+01 angle pdb=" CB GLU G 91 " pdb=" CG GLU G 91 " pdb=" CD GLU G 91 " ideal model delta sigma weight residual 112.60 119.68 -7.08 1.70e+00 3.46e-01 1.73e+01 angle pdb=" CA GLU G 61 " pdb=" CB GLU G 61 " pdb=" CG GLU G 61 " ideal model delta sigma weight residual 114.10 121.60 -7.50 2.00e+00 2.50e-01 1.41e+01 ... (remaining 18682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.80: 5224 28.80 - 57.60: 1786 57.60 - 86.40: 123 86.40 - 115.20: 0 115.20 - 144.00: 5 Dihedral angle restraints: 7138 sinusoidal: 4890 harmonic: 2248 Sorted by residual: dihedral pdb=" CA PHE E 84 " pdb=" C PHE E 84 " pdb=" N GLN E 85 " pdb=" CA GLN E 85 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" C4' DT I 92 " pdb=" C3' DT I 92 " pdb=" O3' DT I 92 " pdb=" P DT I 93 " ideal model delta sinusoidal sigma weight residual 220.00 76.00 144.00 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" C4' DC I 13 " pdb=" C3' DC I 13 " pdb=" O3' DC I 13 " pdb=" P DT I 14 " ideal model delta sinusoidal sigma weight residual 220.00 76.90 143.10 1 3.50e+01 8.16e-04 1.41e+01 ... (remaining 7135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1420 0.041 - 0.082: 553 0.082 - 0.123: 116 0.123 - 0.164: 27 0.164 - 0.204: 5 Chirality restraints: 2121 Sorted by residual: chirality pdb=" C3' DT I 87 " pdb=" C4' DT I 87 " pdb=" O3' DT I 87 " pdb=" C2' DT I 87 " both_signs ideal model delta sigma weight residual False -2.66 -2.46 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB VAL D 108 " pdb=" CA VAL D 108 " pdb=" CG1 VAL D 108 " pdb=" CG2 VAL D 108 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.69e-01 chirality pdb=" CB VAL H 108 " pdb=" CA VAL H 108 " pdb=" CG1 VAL H 108 " pdb=" CG2 VAL H 108 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.69e-01 ... (remaining 2118 not shown) Planarity restraints: 1359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.046 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO C 80 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 120 " 0.045 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO A 121 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.045 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO G 80 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.038 5.00e-02 4.00e+02 ... (remaining 1356 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 799 2.72 - 3.27: 10004 3.27 - 3.81: 23673 3.81 - 4.36: 29233 4.36 - 4.90: 41366 Nonbonded interactions: 105075 Sorted by model distance: nonbonded pdb=" OE1 GLU C 61 " pdb=" CD2 LEU D 103 " model vdw 2.178 3.460 nonbonded pdb=" O ASP B 68 " pdb=" OG1 THR B 71 " model vdw 2.198 3.040 nonbonded pdb=" OE2 GLU C 61 " pdb=" CD2 LEU D 103 " model vdw 2.253 3.460 nonbonded pdb=" CE1 TYR B 98 " pdb=" OD2 ASP H 65 " model vdw 2.293 3.340 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.309 3.040 ... (remaining 105070 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' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 18 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.890 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 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 : 0.006 0.063 12926 Z= 0.260 Angle : 0.848 8.642 18687 Z= 0.513 Chirality : 0.045 0.204 2121 Planarity : 0.007 0.069 1359 Dihedral : 28.192 144.003 5688 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.22), residues: 760 helix: -2.03 (0.16), residues: 535 sheet: None (None), residues: 0 loop : -1.90 (0.34), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 89 TYR 0.012 0.002 TYR G 57 PHE 0.017 0.002 PHE H 62 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00581 (12926) covalent geometry : angle 0.84754 (18687) hydrogen bonds : bond 0.12056 ( 704) hydrogen bonds : angle 4.27089 ( 1766) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.315 Fit side-chains REVERT: E 122 LYS cc_start: 0.7991 (ptmt) cc_final: 0.7660 (ptpp) REVERT: F 45 ARG cc_start: 0.8109 (mmm-85) cc_final: 0.7885 (mtp85) REVERT: G 77 ARG cc_start: 0.6348 (ttp-170) cc_final: 0.5995 (mtm180) REVERT: H 76 ARG cc_start: 0.8101 (ptp90) cc_final: 0.7812 (ptp90) REVERT: H 112 THR cc_start: 0.8775 (p) cc_final: 0.8550 (p) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1975 time to fit residues: 44.1009 Evaluate side-chains 112 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 108 ASN A 113 HIS A 125 GLN D 60 ASN D 92 GLN E 68 GLN E 108 ASN F 25 ASN F 75 HIS G 73 ASN H 46 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.158349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.117565 restraints weight = 18820.478| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.26 r_work: 0.3319 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12926 Z= 0.163 Angle : 0.589 5.966 18687 Z= 0.359 Chirality : 0.034 0.148 2121 Planarity : 0.005 0.048 1359 Dihedral : 31.165 147.638 4132 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.40 % Allowed : 8.37 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.27), residues: 760 helix: 0.13 (0.21), residues: 528 sheet: None (None), residues: 0 loop : -1.42 (0.34), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 71 TYR 0.012 0.001 TYR F 88 PHE 0.010 0.001 PHE H 62 HIS 0.006 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00361 (12926) covalent geometry : angle 0.58872 (18687) hydrogen bonds : bond 0.03983 ( 704) hydrogen bonds : angle 2.90163 ( 1766) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.329 Fit side-chains REVERT: B 53 GLU cc_start: 0.7537 (tt0) cc_final: 0.7323 (mt-10) REVERT: B 68 ASP cc_start: 0.8017 (m-30) cc_final: 0.7737 (m-30) REVERT: C 73 ASN cc_start: 0.8536 (t0) cc_final: 0.8052 (t0) REVERT: C 75 LYS cc_start: 0.8178 (mmtm) cc_final: 0.7866 (mptt) REVERT: E 41 TYR cc_start: 0.7266 (m-10) cc_final: 0.7048 (m-80) REVERT: F 84 MET cc_start: 0.8080 (mmp) cc_final: 0.7832 (mmm) outliers start: 9 outliers final: 3 residues processed: 132 average time/residue: 0.1481 time to fit residues: 25.9832 Evaluate side-chains 111 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 0 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 overall best weight: 4.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS E 76 GLN F 25 ASN G 73 ASN H 81 ASN H 92 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.155251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.114381 restraints weight = 18816.349| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.21 r_work: 0.3268 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12926 Z= 0.221 Angle : 0.632 5.674 18687 Z= 0.377 Chirality : 0.036 0.138 2121 Planarity : 0.005 0.044 1359 Dihedral : 31.285 143.487 4132 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.86 % Allowed : 10.23 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.28), residues: 760 helix: 0.49 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.17 (0.37), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 11 TYR 0.015 0.002 TYR A 54 PHE 0.018 0.002 PHE A 84 HIS 0.005 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00501 (12926) covalent geometry : angle 0.63235 (18687) hydrogen bonds : bond 0.04481 ( 704) hydrogen bonds : angle 2.96957 ( 1766) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: B 68 ASP cc_start: 0.7974 (m-30) cc_final: 0.7705 (m-30) REVERT: C 73 ASN cc_start: 0.8594 (t0) cc_final: 0.8262 (t0) REVERT: C 75 LYS cc_start: 0.8330 (mmtm) cc_final: 0.8060 (mptt) REVERT: D 105 LYS cc_start: 0.8621 (ptpp) cc_final: 0.8379 (ptmm) REVERT: D 113 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8481 (pttm) REVERT: F 59 LYS cc_start: 0.8734 (tmtt) cc_final: 0.8451 (tmtt) REVERT: H 103 LEU cc_start: 0.9343 (mt) cc_final: 0.9033 (mp) outliers start: 12 outliers final: 5 residues processed: 123 average time/residue: 0.1391 time to fit residues: 23.0980 Evaluate side-chains 119 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 70 optimal weight: 4.9990 chunk 35 optimal weight: 0.0570 chunk 79 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 78 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 7 optimal weight: 0.2980 chunk 28 optimal weight: 6.9990 overall best weight: 2.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.158187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.117465 restraints weight = 18832.794| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.25 r_work: 0.3315 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12926 Z= 0.155 Angle : 0.569 5.436 18687 Z= 0.347 Chirality : 0.033 0.142 2121 Planarity : 0.004 0.043 1359 Dihedral : 30.947 147.861 4132 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.86 % Allowed : 12.40 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.29), residues: 760 helix: 1.15 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -1.05 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 35 TYR 0.010 0.001 TYR A 54 PHE 0.010 0.001 PHE A 84 HIS 0.004 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00342 (12926) covalent geometry : angle 0.56940 (18687) hydrogen bonds : bond 0.03684 ( 704) hydrogen bonds : angle 2.70428 ( 1766) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: B 68 ASP cc_start: 0.8043 (m-30) cc_final: 0.7753 (m-30) REVERT: B 79 LYS cc_start: 0.8403 (mmtt) cc_final: 0.8047 (mppt) REVERT: C 73 ASN cc_start: 0.8514 (t0) cc_final: 0.8136 (t0) REVERT: C 75 LYS cc_start: 0.8342 (mmtm) cc_final: 0.8077 (mptt) REVERT: D 105 LYS cc_start: 0.8566 (ptpp) cc_final: 0.8365 (mtmm) REVERT: F 24 ASP cc_start: 0.7404 (t0) cc_final: 0.7149 (t0) REVERT: H 73 GLU cc_start: 0.8254 (tp30) cc_final: 0.7994 (tp30) outliers start: 12 outliers final: 7 residues processed: 122 average time/residue: 0.1475 time to fit residues: 24.1716 Evaluate side-chains 118 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 85 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 90 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.155613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.114549 restraints weight = 19032.676| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.27 r_work: 0.3267 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12926 Z= 0.186 Angle : 0.594 5.477 18687 Z= 0.358 Chirality : 0.035 0.133 2121 Planarity : 0.004 0.042 1359 Dihedral : 30.975 144.452 4132 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.71 % Allowed : 12.56 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.29), residues: 760 helix: 1.22 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -0.95 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 11 TYR 0.014 0.001 TYR A 54 PHE 0.015 0.002 PHE A 84 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00420 (12926) covalent geometry : angle 0.59377 (18687) hydrogen bonds : bond 0.04093 ( 704) hydrogen bonds : angle 2.81326 ( 1766) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.257 Fit side-chains REVERT: B 68 ASP cc_start: 0.7863 (m-30) cc_final: 0.7586 (m-30) REVERT: B 79 LYS cc_start: 0.8378 (mmtt) cc_final: 0.8000 (mppt) REVERT: C 73 ASN cc_start: 0.8303 (t0) cc_final: 0.8005 (t0) REVERT: D 102 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8217 (mm-30) REVERT: D 105 LYS cc_start: 0.8529 (ptpp) cc_final: 0.8295 (mtmm) REVERT: F 35 ARG cc_start: 0.8255 (mtp85) cc_final: 0.7939 (mmm160) REVERT: H 102 GLU cc_start: 0.8283 (mp0) cc_final: 0.8047 (mp0) outliers start: 11 outliers final: 9 residues processed: 118 average time/residue: 0.1306 time to fit residues: 20.9359 Evaluate side-chains 117 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 79 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 90 optimal weight: 20.0000 chunk 75 optimal weight: 30.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.156674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.115910 restraints weight = 18801.775| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.27 r_work: 0.3290 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12926 Z= 0.153 Angle : 0.580 6.985 18687 Z= 0.351 Chirality : 0.034 0.248 2121 Planarity : 0.004 0.041 1359 Dihedral : 30.945 145.135 4132 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.55 % Allowed : 13.49 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.29), residues: 760 helix: 1.43 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.93 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 83 TYR 0.012 0.001 TYR H 80 PHE 0.010 0.001 PHE A 84 HIS 0.002 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00336 (12926) covalent geometry : angle 0.58039 (18687) hydrogen bonds : bond 0.03809 ( 704) hydrogen bonds : angle 2.75899 ( 1766) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.245 Fit side-chains REVERT: B 68 ASP cc_start: 0.8142 (m-30) cc_final: 0.7897 (m-30) REVERT: B 79 LYS cc_start: 0.8369 (mmtt) cc_final: 0.8022 (mppt) REVERT: C 73 ASN cc_start: 0.8430 (t0) cc_final: 0.8206 (t0) REVERT: D 105 LYS cc_start: 0.8608 (ptpp) cc_final: 0.8368 (mtmm) REVERT: F 35 ARG cc_start: 0.8418 (mtp85) cc_final: 0.8060 (mmm160) outliers start: 10 outliers final: 9 residues processed: 118 average time/residue: 0.1422 time to fit residues: 22.3543 Evaluate side-chains 116 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 20 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 28 optimal weight: 30.0000 chunk 84 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.157062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.116299 restraints weight = 18913.541| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.25 r_work: 0.3295 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12926 Z= 0.156 Angle : 0.570 5.399 18687 Z= 0.347 Chirality : 0.034 0.156 2121 Planarity : 0.004 0.041 1359 Dihedral : 30.885 146.239 4132 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.02 % Allowed : 13.33 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.30), residues: 760 helix: 1.61 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.89 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 83 TYR 0.011 0.001 TYR A 54 PHE 0.009 0.001 PHE A 84 HIS 0.002 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00345 (12926) covalent geometry : angle 0.57008 (18687) hydrogen bonds : bond 0.03762 ( 704) hydrogen bonds : angle 2.72306 ( 1766) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.204 Fit side-chains REVERT: B 68 ASP cc_start: 0.7880 (m-30) cc_final: 0.7631 (m-30) REVERT: B 79 LYS cc_start: 0.8313 (mmtt) cc_final: 0.7953 (mppt) REVERT: D 105 LYS cc_start: 0.8516 (ptpp) cc_final: 0.8287 (mtmm) REVERT: F 24 ASP cc_start: 0.7112 (t0) cc_final: 0.6851 (t0) REVERT: F 35 ARG cc_start: 0.8213 (mtp85) cc_final: 0.7828 (mmm160) outliers start: 13 outliers final: 10 residues processed: 112 average time/residue: 0.1327 time to fit residues: 20.2016 Evaluate side-chains 117 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 82 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 60 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 87 optimal weight: 30.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.156938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.116210 restraints weight = 18809.916| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.25 r_work: 0.3291 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12926 Z= 0.168 Angle : 0.578 5.476 18687 Z= 0.351 Chirality : 0.034 0.147 2121 Planarity : 0.004 0.041 1359 Dihedral : 30.848 146.758 4132 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.86 % Allowed : 13.33 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.29), residues: 760 helix: 1.60 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.87 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 83 TYR 0.025 0.002 TYR F 88 PHE 0.011 0.001 PHE A 84 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00374 (12926) covalent geometry : angle 0.57821 (18687) hydrogen bonds : bond 0.03878 ( 704) hydrogen bonds : angle 2.76087 ( 1766) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.302 Fit side-chains REVERT: A 79 LYS cc_start: 0.8071 (tttt) cc_final: 0.7837 (mttt) REVERT: B 68 ASP cc_start: 0.8083 (m-30) cc_final: 0.7792 (m-30) REVERT: D 79 HIS cc_start: 0.7707 (t-170) cc_final: 0.7458 (t-170) REVERT: D 105 LYS cc_start: 0.8624 (ptpp) cc_final: 0.8380 (ptmm) REVERT: F 24 ASP cc_start: 0.7370 (t0) cc_final: 0.6992 (t0) REVERT: F 35 ARG cc_start: 0.8398 (mtp85) cc_final: 0.7987 (mmm160) REVERT: H 81 ASN cc_start: 0.8204 (m-40) cc_final: 0.7989 (m-40) outliers start: 12 outliers final: 10 residues processed: 116 average time/residue: 0.1291 time to fit residues: 20.5492 Evaluate side-chains 120 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 65 optimal weight: 0.0470 chunk 97 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 overall best weight: 3.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.156631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.115921 restraints weight = 18747.704| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.25 r_work: 0.3288 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12926 Z= 0.176 Angle : 0.584 5.461 18687 Z= 0.353 Chirality : 0.034 0.145 2121 Planarity : 0.004 0.041 1359 Dihedral : 30.845 148.515 4132 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.86 % Allowed : 13.49 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.29), residues: 760 helix: 1.61 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.85 (0.38), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 83 TYR 0.022 0.002 TYR F 88 PHE 0.012 0.001 PHE A 84 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00396 (12926) covalent geometry : angle 0.58415 (18687) hydrogen bonds : bond 0.03979 ( 704) hydrogen bonds : angle 2.80254 ( 1766) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.234 Fit side-chains REVERT: B 68 ASP cc_start: 0.8160 (m-30) cc_final: 0.7894 (m-30) REVERT: D 79 HIS cc_start: 0.7786 (t-170) cc_final: 0.7541 (t-170) REVERT: D 105 LYS cc_start: 0.8626 (ptpp) cc_final: 0.8411 (mtmm) REVERT: F 35 ARG cc_start: 0.8385 (mtp85) cc_final: 0.7857 (mmm160) outliers start: 12 outliers final: 11 residues processed: 115 average time/residue: 0.1218 time to fit residues: 19.4041 Evaluate side-chains 117 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 16 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS C 73 ASN G 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.155866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.115089 restraints weight = 18837.623| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.25 r_work: 0.3274 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12926 Z= 0.191 Angle : 0.601 5.708 18687 Z= 0.361 Chirality : 0.035 0.142 2121 Planarity : 0.004 0.041 1359 Dihedral : 30.892 150.586 4132 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.02 % Allowed : 13.64 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.29), residues: 760 helix: 1.53 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.85 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 83 TYR 0.020 0.002 TYR F 88 PHE 0.013 0.001 PHE A 84 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00432 (12926) covalent geometry : angle 0.60122 (18687) hydrogen bonds : bond 0.04169 ( 704) hydrogen bonds : angle 2.87706 ( 1766) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.220 Fit side-chains REVERT: B 68 ASP cc_start: 0.8166 (m-30) cc_final: 0.7895 (m-30) REVERT: D 79 HIS cc_start: 0.7798 (t-170) cc_final: 0.7563 (t-170) REVERT: D 105 LYS cc_start: 0.8626 (ptpp) cc_final: 0.8386 (ptmm) REVERT: F 24 ASP cc_start: 0.7411 (t0) cc_final: 0.7046 (t0) REVERT: F 35 ARG cc_start: 0.8386 (mtp85) cc_final: 0.7993 (mmm160) REVERT: H 56 MET cc_start: 0.8554 (tpp) cc_final: 0.8268 (mmm) outliers start: 13 outliers final: 11 residues processed: 114 average time/residue: 0.1296 time to fit residues: 20.0422 Evaluate side-chains 117 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 45 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN D 81 ASN G 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.156015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.115459 restraints weight = 18719.083| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.24 r_work: 0.3279 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12926 Z= 0.178 Angle : 0.595 5.609 18687 Z= 0.358 Chirality : 0.034 0.140 2121 Planarity : 0.004 0.041 1359 Dihedral : 30.887 150.798 4132 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.86 % Allowed : 13.95 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.29), residues: 760 helix: 1.52 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.79 (0.38), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 83 TYR 0.016 0.002 TYR H 80 PHE 0.011 0.001 PHE A 84 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00400 (12926) covalent geometry : angle 0.59519 (18687) hydrogen bonds : bond 0.04086 ( 704) hydrogen bonds : angle 2.85793 ( 1766) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2922.16 seconds wall clock time: 50 minutes 38.60 seconds (3038.60 seconds total)