Starting phenix.real_space_refine on Wed Aug 5 23:42:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v28_42901/08_2026/8v28_42901_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v28_42901/08_2026/8v28_42901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v28_42901/08_2026/8v28_42901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v28_42901/08_2026/8v28_42901.map" model { file = "/net/cci-nas-00/data/ceres_data/8v28_42901/08_2026/8v28_42901_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v28_42901/08_2026/8v28_42901_neut.cif" } resolution = 3.36 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= 0.002 sd= 0.019 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 288 5.49 5 S 15 5.16 5 C 7046 2.51 5 N 2380 2.21 5 O 2930 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12659 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 859 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "D" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 764 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 817 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 841 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 754 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Time building chain proxies: 2.46, per 1000 atoms: 0.19 Number of scatterers: 12659 At special positions: 0 Unit cell: (100.88, 122.22, 118.34, 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 15 16.00 P 288 15.00 O 2930 8.00 N 2380 7.00 C 7046 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: 0.91 Conformation dependent library (CDL) restraints added in 282.9 milliseconds 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1586 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 67.0% alpha, 4.3% beta 139 base pairs and 250 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.829A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.772A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.653A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.171A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.562A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.631A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.518A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.657A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.645A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.564A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.717A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.520A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.176A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.551A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.595A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.545A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.576A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing helix chain 'K' and resid 22 through 35 Processing helix chain 'K' and resid 37 through 41 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.952A 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: 7.330A 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: 6.738A 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: 7.385A 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 'K' and resid 12 through 16 421 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 357 hydrogen bonds 714 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 250 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 1.25 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: 2434 1.33 - 1.45: 4277 1.45 - 1.57: 6155 1.57 - 1.69: 576 1.69 - 1.81: 26 Bond restraints: 13468 Sorted by residual: bond pdb=" C1' DG I -70 " pdb=" N9 DG I -70 " ideal model delta sigma weight residual 1.468 1.384 0.084 1.40e-02 5.10e+03 3.62e+01 bond pdb=" C1' DG J -70 " pdb=" N9 DG J -70 " ideal model delta sigma weight residual 1.468 1.386 0.082 1.40e-02 5.10e+03 3.43e+01 bond pdb=" C1' DA I 72 " pdb=" N9 DA I 72 " ideal model delta sigma weight residual 1.468 1.390 0.078 1.40e-02 5.10e+03 3.13e+01 bond pdb=" C1' DT I -72 " pdb=" N1 DT I -72 " ideal model delta sigma weight residual 1.468 1.546 -0.078 1.40e-02 5.10e+03 3.11e+01 bond pdb=" C1' DT J -72 " pdb=" N1 DT J -72 " ideal model delta sigma weight residual 1.468 1.545 -0.077 1.40e-02 5.10e+03 3.05e+01 ... (remaining 13463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 18775 2.03 - 4.06: 621 4.06 - 6.09: 23 6.09 - 8.12: 2 8.12 - 10.15: 5 Bond angle restraints: 19426 Sorted by residual: angle pdb=" C3' DG J 71 " pdb=" O3' DG J 71 " pdb=" P DA J 72 " ideal model delta sigma weight residual 119.70 109.55 10.15 1.20e+00 6.94e-01 7.16e+01 angle pdb=" C3' DC J 70 " pdb=" O3' DC J 70 " pdb=" P DG J 71 " ideal model delta sigma weight residual 119.70 109.76 9.94 1.20e+00 6.94e-01 6.86e+01 angle pdb=" C3' DT J 69 " pdb=" O3' DT J 69 " pdb=" P DC J 70 " ideal model delta sigma weight residual 119.70 110.58 9.12 1.20e+00 6.94e-01 5.78e+01 angle pdb=" O4' DG J 32 " pdb=" C4' DG J 32 " pdb=" C3' DG J 32 " ideal model delta sigma weight residual 106.00 103.27 2.73 6.00e-01 2.78e+00 2.08e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 ... (remaining 19421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 6009 35.66 - 71.32: 1362 71.32 - 106.98: 13 106.98 - 142.65: 4 142.65 - 178.31: 1 Dihedral angle restraints: 7389 sinusoidal: 4936 harmonic: 2453 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 38.31 -178.31 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J 54 " pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sinusoidal sigma weight residual 220.00 91.35 128.65 1 3.50e+01 8.16e-04 1.27e+01 dihedral pdb=" C4' DC J 34 " pdb=" C3' DC J 34 " pdb=" O3' DC J 34 " pdb=" P DT J 35 " ideal model delta sinusoidal sigma weight residual 220.00 95.57 124.43 1 3.50e+01 8.16e-04 1.23e+01 ... (remaining 7386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2103 0.095 - 0.190: 109 0.190 - 0.286: 0 0.286 - 0.381: 0 0.381 - 0.476: 3 Chirality restraints: 2215 Sorted by residual: chirality pdb=" P DC J 70 " pdb=" OP1 DC J 70 " pdb=" OP2 DC J 70 " pdb=" O5' DC J 70 " both_signs ideal model delta sigma weight residual True 2.34 -2.81 -0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" P DG J 71 " pdb=" OP1 DG J 71 " pdb=" OP2 DG J 71 " pdb=" O5' DG J 71 " both_signs ideal model delta sigma weight residual True 2.34 -2.80 -0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" P DA J 72 " pdb=" OP1 DA J 72 " pdb=" OP2 DA J 72 " pdb=" O5' DA J 72 " both_signs ideal model delta sigma weight residual True 2.34 -2.80 -0.46 2.00e-01 2.50e+01 5.33e+00 ... (remaining 2212 not shown) Planarity restraints: 1457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 24 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C ASP F 24 " -0.044 2.00e-02 2.50e+03 pdb=" O ASP F 24 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN F 25 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 24 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.18e+00 pdb=" CG ASP F 24 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP F 24 " 0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP F 24 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.024 2.00e-02 2.50e+03 1.00e-02 3.01e+00 pdb=" N9 DG I 47 " 0.022 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " -0.005 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.002 2.00e-02 2.50e+03 ... (remaining 1454 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 2842 2.82 - 3.34: 10531 3.34 - 3.86: 22604 3.86 - 4.38: 26544 4.38 - 4.90: 38192 Nonbonded interactions: 100713 Sorted by model distance: nonbonded pdb=" O THR E 58 " pdb=" OG1 THR E 58 " model vdw 2.295 3.040 nonbonded pdb=" O GLN K 2 " pdb=" N GLU K 64 " model vdw 2.347 3.120 nonbonded pdb=" O ARG A 129 " pdb=" NH1 ARG A 129 " model vdw 2.361 3.120 nonbonded pdb=" N ASP F 85 " pdb=" OD1 ASP F 85 " model vdw 2.362 3.120 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.376 3.040 ... (remaining 100708 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 37 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 10 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 26 through 121) 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.450 Find NCS groups from input model: 0.100 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 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 0.084 13468 Z= 0.537 Angle : 0.742 10.154 19426 Z= 0.653 Chirality : 0.047 0.476 2215 Planarity : 0.004 0.037 1457 Dihedral : 27.274 178.308 5803 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.56 % Allowed : 19.15 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.30), residues: 827 helix: 3.33 (0.22), residues: 530 sheet: 1.37 (1.73), residues: 12 loop : -1.10 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 96 TYR 0.017 0.001 TYR H 80 PHE 0.010 0.001 PHE F 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.54 (13468) covalent geometry : angle 0.74172 / 0.65 (19426) hydrogen bonds : bond 0.11556 / 7.68 ( 778) hydrogen bonds : angle 3.58914 / 2.47 ( 1950) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 0.249 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 114 average time/residue: 0.1414 time to fit residues: 21.1535 Evaluate side-chains 110 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN E 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.091747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.060202 restraints weight = 29974.138| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.06 r_work: 0.2640 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.0648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13468 Z= 0.205 Angle : 0.630 8.511 19426 Z= 0.377 Chirality : 0.046 0.269 2215 Planarity : 0.004 0.049 1457 Dihedral : 29.671 176.952 4112 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.11 % Allowed : 19.01 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.30), residues: 827 helix: 3.32 (0.22), residues: 531 sheet: 1.24 (1.30), residues: 20 loop : -1.09 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 96 TYR 0.014 0.001 TYR H 80 PHE 0.011 0.001 PHE D 67 HIS 0.004 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.21 (13468) covalent geometry : angle 0.63020 / 0.38 (19426) hydrogen bonds : bond 0.07281 / 4.83 ( 778) hydrogen bonds : angle 3.26066 / 2.26 ( 1950) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.303 Fit side-chains REVERT: A 83 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8603 (mtp85) REVERT: F 24 ASP cc_start: 0.8530 (p0) cc_final: 0.8273 (p0) REVERT: H 30 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7821 (mmt180) REVERT: H 65 ASP cc_start: 0.8804 (t0) cc_final: 0.8535 (t0) outliers start: 15 outliers final: 8 residues processed: 126 average time/residue: 0.1314 time to fit residues: 21.6734 Evaluate side-chains 116 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 67 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 101 optimal weight: 30.0000 chunk 63 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.093750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.062546 restraints weight = 30346.537| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.09 r_work: 0.2697 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.0733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13468 Z= 0.143 Angle : 0.562 7.936 19426 Z= 0.344 Chirality : 0.042 0.259 2215 Planarity : 0.004 0.036 1457 Dihedral : 29.712 177.449 4110 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.11 % Allowed : 19.86 % Favored : 78.03 % 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: 3.10 (0.30), residues: 827 helix: 3.51 (0.22), residues: 530 sheet: 1.56 (1.35), residues: 20 loop : -1.02 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 96 TYR 0.007 0.001 TYR H 80 PHE 0.008 0.001 PHE D 67 HIS 0.003 0.001 HIS K 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.14 (13468) covalent geometry : angle 0.56158 / 0.34 (19426) hydrogen bonds : bond 0.05891 / 3.90 ( 778) hydrogen bonds : angle 2.95804 / 2.04 ( 1950) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.283 Fit side-chains REVERT: A 83 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8634 (mtp85) REVERT: D 73 GLU cc_start: 0.9126 (tp30) cc_final: 0.8910 (tp30) REVERT: F 24 ASP cc_start: 0.8529 (p0) cc_final: 0.8209 (p0) REVERT: F 74 GLU cc_start: 0.8762 (tp30) cc_final: 0.8405 (mt-10) REVERT: H 65 ASP cc_start: 0.8881 (t0) cc_final: 0.8637 (t0) outliers start: 15 outliers final: 7 residues processed: 125 average time/residue: 0.1254 time to fit residues: 20.9461 Evaluate side-chains 115 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 69 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 4 optimal weight: 0.3980 chunk 95 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.094422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.063410 restraints weight = 30260.610| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.07 r_work: 0.2714 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13468 Z= 0.140 Angle : 0.550 7.827 19426 Z= 0.334 Chirality : 0.041 0.247 2215 Planarity : 0.004 0.058 1457 Dihedral : 29.837 176.896 4110 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.82 % Allowed : 19.86 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.18 (0.30), residues: 827 helix: 3.59 (0.22), residues: 531 sheet: 1.42 (1.32), residues: 20 loop : -1.03 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 42 TYR 0.011 0.001 TYR H 80 PHE 0.008 0.001 PHE F 61 HIS 0.002 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.14 (13468) covalent geometry : angle 0.55002 / 0.33 (19426) hydrogen bonds : bond 0.05495 / 3.64 ( 778) hydrogen bonds : angle 2.87000 / 1.98 ( 1950) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.320 Fit side-chains REVERT: A 83 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8653 (mtp85) REVERT: D 73 GLU cc_start: 0.9147 (tp30) cc_final: 0.8846 (tp30) REVERT: F 24 ASP cc_start: 0.8538 (p0) cc_final: 0.8240 (p0) REVERT: H 30 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7816 (mmt180) REVERT: H 65 ASP cc_start: 0.8868 (t0) cc_final: 0.8608 (t0) outliers start: 20 outliers final: 10 residues processed: 131 average time/residue: 0.1286 time to fit residues: 22.3023 Evaluate side-chains 122 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 70 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 80 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.094697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.063835 restraints weight = 30440.101| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.08 r_work: 0.2725 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13468 Z= 0.136 Angle : 0.544 7.776 19426 Z= 0.330 Chirality : 0.041 0.245 2215 Planarity : 0.004 0.046 1457 Dihedral : 29.877 176.966 4110 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.11 % Allowed : 20.85 % Favored : 77.04 % 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: 3.19 (0.30), residues: 827 helix: 3.62 (0.22), residues: 531 sheet: 1.35 (1.31), residues: 20 loop : -1.06 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 96 TYR 0.010 0.001 TYR H 80 PHE 0.008 0.001 PHE D 67 HIS 0.002 0.000 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.14 (13468) covalent geometry : angle 0.54357 / 0.33 (19426) hydrogen bonds : bond 0.05265 / 3.48 ( 778) hydrogen bonds : angle 2.80740 / 1.94 ( 1950) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.253 Fit side-chains REVERT: B 24 ASP cc_start: 0.8224 (t70) cc_final: 0.7972 (t70) REVERT: D 73 GLU cc_start: 0.9171 (tp30) cc_final: 0.8865 (tp30) REVERT: D 110 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8499 (mm-30) REVERT: F 24 ASP cc_start: 0.8538 (p0) cc_final: 0.8190 (p0) REVERT: H 30 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7854 (mmt180) REVERT: H 32 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: H 65 ASP cc_start: 0.8862 (t0) cc_final: 0.8586 (t0) outliers start: 15 outliers final: 10 residues processed: 122 average time/residue: 0.1329 time to fit residues: 21.5318 Evaluate side-chains 121 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 84 optimal weight: 20.0000 chunk 56 optimal weight: 0.9980 chunk 78 optimal weight: 20.0000 chunk 22 optimal weight: 4.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.094049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.062800 restraints weight = 30152.584| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.12 r_work: 0.2705 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13468 Z= 0.145 Angle : 0.552 7.914 19426 Z= 0.331 Chirality : 0.041 0.241 2215 Planarity : 0.004 0.052 1457 Dihedral : 29.946 176.799 4110 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.25 % Allowed : 20.85 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.14 (0.30), residues: 827 helix: 3.61 (0.22), residues: 532 sheet: 1.26 (1.31), residues: 20 loop : -1.18 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 96 TYR 0.010 0.001 TYR H 80 PHE 0.008 0.001 PHE F 61 HIS 0.002 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.15 (13468) covalent geometry : angle 0.55227 / 0.33 (19426) hydrogen bonds : bond 0.05564 / 3.69 ( 778) hydrogen bonds : angle 2.84180 / 1.96 ( 1950) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.302 Fit side-chains REVERT: A 59 GLU cc_start: 0.8246 (pm20) cc_final: 0.7919 (pm20) REVERT: D 73 GLU cc_start: 0.9178 (tp30) cc_final: 0.8802 (tp30) REVERT: D 110 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8518 (mm-30) REVERT: F 24 ASP cc_start: 0.8560 (p0) cc_final: 0.8224 (p0) REVERT: H 30 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7853 (mmt180) REVERT: H 32 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: H 65 ASP cc_start: 0.8895 (t0) cc_final: 0.8617 (t0) outliers start: 16 outliers final: 11 residues processed: 125 average time/residue: 0.1341 time to fit residues: 22.3932 Evaluate side-chains 123 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 82 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 74 optimal weight: 20.0000 chunk 102 optimal weight: 0.0060 chunk 93 optimal weight: 10.0000 chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 30.0000 chunk 24 optimal weight: 0.9990 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.093145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.061829 restraints weight = 29925.873| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.09 r_work: 0.2680 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13468 Z= 0.160 Angle : 0.573 8.099 19426 Z= 0.339 Chirality : 0.042 0.240 2215 Planarity : 0.004 0.035 1457 Dihedral : 30.008 176.924 4110 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.96 % Allowed : 20.42 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.04 (0.30), residues: 827 helix: 3.56 (0.22), residues: 532 sheet: 1.07 (1.31), residues: 20 loop : -1.25 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 96 TYR 0.010 0.001 TYR H 80 PHE 0.009 0.001 PHE F 61 HIS 0.003 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 (13468) covalent geometry : angle 0.57296 / 0.34 (19426) hydrogen bonds : bond 0.06045 / 4.01 ( 778) hydrogen bonds : angle 2.91223 / 2.03 ( 1950) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.209 Fit side-chains REVERT: A 59 GLU cc_start: 0.8296 (pm20) cc_final: 0.7972 (pm20) REVERT: D 32 GLU cc_start: 0.8429 (mp0) cc_final: 0.8180 (mp0) REVERT: D 73 GLU cc_start: 0.9163 (tp30) cc_final: 0.8737 (tp30) REVERT: D 110 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8553 (mm-30) REVERT: F 24 ASP cc_start: 0.8532 (p0) cc_final: 0.8194 (p0) REVERT: H 30 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7959 (mmt180) REVERT: H 32 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7640 (mm-30) REVERT: H 65 ASP cc_start: 0.8940 (t0) cc_final: 0.8650 (t0) outliers start: 21 outliers final: 14 residues processed: 125 average time/residue: 0.1202 time to fit residues: 20.4519 Evaluate side-chains 124 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 83 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 94 optimal weight: 20.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.093283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.061937 restraints weight = 29682.446| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.08 r_work: 0.2683 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13468 Z= 0.152 Angle : 0.565 8.088 19426 Z= 0.335 Chirality : 0.042 0.242 2215 Planarity : 0.004 0.036 1457 Dihedral : 30.013 176.918 4110 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.82 % Allowed : 20.85 % Favored : 76.34 % 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: 3.03 (0.30), residues: 827 helix: 3.55 (0.22), residues: 532 sheet: 1.51 (1.29), residues: 19 loop : -1.28 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 96 TYR 0.008 0.001 TYR H 80 PHE 0.009 0.001 PHE F 61 HIS 0.002 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 (13468) covalent geometry : angle 0.56525 / 0.34 (19426) hydrogen bonds : bond 0.05955 / 3.95 ( 778) hydrogen bonds : angle 2.89939 / 2.01 ( 1950) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.241 Fit side-chains REVERT: A 59 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8023 (pm20) REVERT: D 73 GLU cc_start: 0.9163 (tp30) cc_final: 0.8738 (tp30) REVERT: D 110 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8541 (mm-30) REVERT: F 24 ASP cc_start: 0.8534 (p0) cc_final: 0.8189 (p0) REVERT: F 39 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8895 (mmt90) REVERT: H 30 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7958 (mmt180) REVERT: H 32 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7634 (mm-30) REVERT: H 65 ASP cc_start: 0.8935 (t0) cc_final: 0.8644 (t0) outliers start: 20 outliers final: 15 residues processed: 122 average time/residue: 0.1241 time to fit residues: 20.5167 Evaluate side-chains 125 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 46 optimal weight: 0.0770 chunk 78 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 overall best weight: 5.4148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.087586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.055926 restraints weight = 30121.085| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 2.02 r_work: 0.2539 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 13468 Z= 0.350 Angle : 0.785 9.476 19426 Z= 0.433 Chirality : 0.055 0.249 2215 Planarity : 0.006 0.050 1457 Dihedral : 30.218 177.939 4110 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.38 % Allowed : 20.14 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.29), residues: 827 helix: 2.76 (0.22), residues: 533 sheet: 0.96 (1.33), residues: 20 loop : -1.61 (0.33), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 96 TYR 0.025 0.002 TYR H 80 PHE 0.023 0.002 PHE D 67 HIS 0.006 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00805 / 0.35 (13468) covalent geometry : angle 0.78496 / 0.43 (19426) hydrogen bonds : bond 0.10088 / 6.74 ( 778) hydrogen bonds : angle 3.69527 / 2.60 ( 1950) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.250 Fit side-chains REVERT: D 73 GLU cc_start: 0.9213 (tp30) cc_final: 0.8849 (tp30) REVERT: D 110 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8382 (mm-30) REVERT: F 24 ASP cc_start: 0.8587 (p0) cc_final: 0.8238 (p0) REVERT: H 30 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7872 (mmt180) REVERT: H 32 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7746 (mm-30) outliers start: 24 outliers final: 17 residues processed: 119 average time/residue: 0.1417 time to fit residues: 22.5027 Evaluate side-chains 121 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 5 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 4 optimal weight: 0.0170 chunk 101 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.093690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.061781 restraints weight = 29778.118| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.10 r_work: 0.2673 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13468 Z= 0.142 Angle : 0.591 8.922 19426 Z= 0.349 Chirality : 0.042 0.268 2215 Planarity : 0.004 0.036 1457 Dihedral : 30.008 178.342 4110 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.83 % Allowed : 21.69 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.30), residues: 827 helix: 3.36 (0.22), residues: 532 sheet: 1.36 (1.29), residues: 19 loop : -1.40 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 96 TYR 0.006 0.001 TYR G 50 PHE 0.011 0.001 PHE B 61 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.14 (13468) covalent geometry : angle 0.59094 / 0.35 (19426) hydrogen bonds : bond 0.06003 / 3.99 ( 778) hydrogen bonds : angle 2.91433 / 2.03 ( 1950) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.323 Fit side-chains REVERT: D 73 GLU cc_start: 0.9164 (tp30) cc_final: 0.8922 (tp30) REVERT: D 110 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8499 (mm-30) REVERT: F 24 ASP cc_start: 0.8555 (p0) cc_final: 0.8213 (p0) REVERT: H 30 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7980 (mmt180) REVERT: H 32 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7674 (mm-30) REVERT: H 65 ASP cc_start: 0.8926 (t0) cc_final: 0.8586 (t0) outliers start: 13 outliers final: 10 residues processed: 124 average time/residue: 0.1259 time to fit residues: 21.1244 Evaluate side-chains 121 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 69 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.091708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.059677 restraints weight = 29518.265| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.10 r_work: 0.2627 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13468 Z= 0.191 Angle : 0.616 8.354 19426 Z= 0.356 Chirality : 0.044 0.245 2215 Planarity : 0.004 0.037 1457 Dihedral : 30.096 178.207 4110 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.69 % Allowed : 22.39 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.30), residues: 827 helix: 3.39 (0.22), residues: 533 sheet: 1.31 (1.33), residues: 19 loop : -1.48 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 96 TYR 0.011 0.001 TYR B 98 PHE 0.010 0.001 PHE D 67 HIS 0.003 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 (13468) covalent geometry : angle 0.61573 / 0.36 (19426) hydrogen bonds : bond 0.06825 / 4.53 ( 778) hydrogen bonds : angle 3.06742 / 2.13 ( 1950) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2073.46 seconds wall clock time: 36 minutes 6.58 seconds (2166.58 seconds total)