Starting phenix.real_space_refine on Wed Feb 4 09:37:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r1d_53505/02_2026/9r1d_53505.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r1d_53505/02_2026/9r1d_53505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9r1d_53505/02_2026/9r1d_53505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r1d_53505/02_2026/9r1d_53505.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r1d_53505/02_2026/9r1d_53505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r1d_53505/02_2026/9r1d_53505.map" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 230 5.49 5 S 20 5.16 5 C 5471 2.51 5 N 1861 2.21 5 O 2298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9880 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 604 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "B" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "C" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 679 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "D" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 685 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "E" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 604 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "F" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 604 Classifications: {'peptide': 76} Link IDs: {'TRANS': 75} Chain: "G" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 685 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "H" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 692 Classifications: {'peptide': 89} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "I" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2375 Classifications: {'DNA': 115} Link IDs: {'rna3p': 114} Chain: "J" Number of atoms: 2340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2340 Classifications: {'DNA': 115} Link IDs: {'rna3p': 114} Time building chain proxies: 1.86, per 1000 atoms: 0.19 Number of scatterers: 9880 At special positions: 0 Unit cell: (80.56, 114.48, 117.66, 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 20 16.00 P 230 15.00 O 2298 8.00 N 1861 7.00 C 5471 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: 0.79 Conformation dependent library (CDL) restraints added in 127.5 milliseconds 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1246 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 7 sheets defined 78.0% alpha, 2.1% beta 107 base pairs and 185 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 66 through 80 Processing helix chain 'A' and resid 88 through 117 Processing helix chain 'A' and resid 123 through 134 removed outlier: 3.633A pdb=" N ILE A 127 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 28 through 40 removed outlier: 3.531A pdb=" N ILE B 32 " --> pdb=" O THR B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 74 removed outlier: 4.054A pdb=" N GLU B 51 " --> pdb=" O VAL B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 91 removed outlier: 3.707A pdb=" N ARG B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 44 through 73 removed outlier: 3.755A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 92 Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'D' and resid 25 through 37 Processing helix chain 'D' and resid 43 through 72 removed outlier: 3.558A pdb=" N ILE D 49 " --> pdb=" O ARG D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 90 removed outlier: 3.504A pdb=" N THR D 84 " --> pdb=" O ARG D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 110 removed outlier: 3.650A pdb=" N LYS D 96 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU D 101 " --> pdb=" O HIS D 97 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 81 removed outlier: 3.529A pdb=" N LEU E 81 " --> pdb=" O VAL E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 117 Processing helix chain 'E' and resid 123 through 135 removed outlier: 3.606A pdb=" N ILE E 127 " --> pdb=" O PHE E 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 27 Processing helix chain 'F' and resid 28 through 39 Processing helix chain 'F' and resid 47 through 74 removed outlier: 4.228A pdb=" N GLU F 51 " --> pdb=" O VAL F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 91 removed outlier: 3.704A pdb=" N ARG F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 44 through 72 removed outlier: 3.656A pdb=" N ALA G 48 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 91 Processing helix chain 'G' and resid 94 through 99 Processing helix chain 'H' and resid 25 through 37 Processing helix chain 'H' and resid 43 through 73 Processing helix chain 'H' and resid 78 through 90 removed outlier: 3.656A pdb=" N LEU H 82 " --> pdb=" O GLY H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 110 removed outlier: 4.258A pdb=" N HIS H 97 " --> pdb=" O ASP H 93 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA H 100 " --> pdb=" O LYS H 96 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87 removed outlier: 6.747A pdb=" N ARG A 86 " --> pdb=" O VAL B 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 122 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.916A pdb=" N ARG C 42 " --> pdb=" O LEU D 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 79 through 80 Processing sheet with id=AA5, first strand: chain 'E' and resid 86 through 87 removed outlier: 6.847A pdb=" N ARG E 86 " --> pdb=" O VAL F 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 121 through 122 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.353A pdb=" N ARG G 42 " --> pdb=" O LEU H 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 371 hydrogen bonds defined for protein. 1101 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 278 hydrogen bonds 556 hydrogen bond angles 0 basepair planarities 107 basepair parallelities 185 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1178 1.32 - 1.44: 3889 1.44 - 1.56: 4950 1.56 - 1.69: 458 1.69 - 1.81: 36 Bond restraints: 10511 Sorted by residual: bond pdb=" C PRO D 91 " pdb=" O PRO D 91 " ideal model delta sigma weight residual 1.235 1.191 0.044 1.30e-02 5.92e+03 1.16e+01 bond pdb=" N VAL D 27 " pdb=" CA VAL D 27 " ideal model delta sigma weight residual 1.461 1.498 -0.036 1.17e-02 7.31e+03 9.71e+00 bond pdb=" N VAL D 89 " pdb=" CA VAL D 89 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.22e-02 6.72e+03 9.26e+00 bond pdb=" N LEU C 23 " pdb=" CA LEU C 23 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.17e-02 7.31e+03 8.95e+00 bond pdb=" N TRP D 25 " pdb=" CA TRP D 25 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.25e-02 6.40e+03 8.27e+00 ... (remaining 10506 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 13970 1.61 - 3.22: 988 3.22 - 4.83: 170 4.83 - 6.44: 36 6.44 - 8.05: 20 Bond angle restraints: 15184 Sorted by residual: angle pdb=" N ILE C 24 " pdb=" CA ILE C 24 " pdb=" C ILE C 24 " ideal model delta sigma weight residual 112.35 106.04 6.31 1.41e+00 5.03e-01 2.01e+01 angle pdb=" CA GLY F 97 " pdb=" C GLY F 97 " pdb=" O GLY F 97 " ideal model delta sigma weight residual 122.24 117.83 4.41 1.08e+00 8.57e-01 1.67e+01 angle pdb=" CB HIS B 83 " pdb=" CG HIS B 83 " pdb=" CD2 HIS B 83 " ideal model delta sigma weight residual 131.20 126.02 5.18 1.30e+00 5.92e-01 1.59e+01 angle pdb=" CA PHE D 58 " pdb=" CB PHE D 58 " pdb=" CG PHE D 58 " ideal model delta sigma weight residual 113.80 117.70 -3.90 1.00e+00 1.00e+00 1.52e+01 angle pdb=" OE1 GLN D 83 " pdb=" CD GLN D 83 " pdb=" NE2 GLN D 83 " ideal model delta sigma weight residual 122.60 118.73 3.87 1.00e+00 1.00e+00 1.50e+01 ... (remaining 15179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.32: 4193 25.32 - 50.63: 1155 50.63 - 75.95: 346 75.95 - 101.26: 3 101.26 - 126.58: 1 Dihedral angle restraints: 5698 sinusoidal: 3779 harmonic: 1919 Sorted by residual: dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 93.42 126.58 1 3.50e+01 8.16e-04 1.25e+01 dihedral pdb=" C ARG D 73 " pdb=" N ARG D 73 " pdb=" CA ARG D 73 " pdb=" CB ARG D 73 " ideal model delta harmonic sigma weight residual -122.60 -131.26 8.66 0 2.50e+00 1.60e-01 1.20e+01 dihedral pdb=" CA ILE D 36 " pdb=" C ILE D 36 " pdb=" N ASN D 37 " pdb=" CA ASN D 37 " ideal model delta harmonic sigma weight residual 180.00 163.02 16.98 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 5695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1699 0.127 - 0.253: 42 0.253 - 0.380: 2 0.380 - 0.506: 0 0.506 - 0.633: 14 Chirality restraints: 1757 Sorted by residual: chirality pdb=" P DG I -56 " pdb=" OP1 DG I -56 " pdb=" OP2 DG I -56 " pdb=" O5' DG I -56 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" P DA I -55 " pdb=" OP1 DA I -55 " pdb=" OP2 DA I -55 " pdb=" O5' DA I -55 " both_signs ideal model delta sigma weight residual True 2.35 -2.95 -0.60 2.00e-01 2.50e+01 9.03e+00 chirality pdb=" P DC I -54 " pdb=" OP1 DC I -54 " pdb=" OP2 DC I -54 " pdb=" O5' DC I -54 " both_signs ideal model delta sigma weight residual True 2.35 -2.94 -0.60 2.00e-01 2.50e+01 8.93e+00 ... (remaining 1754 not shown) Planarity restraints: 1113 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 73 " 0.117 2.00e-02 2.50e+03 5.88e-02 6.91e+01 pdb=" CG TYR B 73 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR B 73 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 TYR B 73 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR B 73 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B 73 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 73 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR B 73 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -33 " 0.080 2.00e-02 2.50e+03 4.54e-02 6.17e+01 pdb=" N9 DG I -33 " -0.027 2.00e-02 2.50e+03 pdb=" C8 DG I -33 " 0.018 2.00e-02 2.50e+03 pdb=" N7 DG I -33 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DG I -33 " -0.029 2.00e-02 2.50e+03 pdb=" C6 DG I -33 " -0.006 2.00e-02 2.50e+03 pdb=" O6 DG I -33 " 0.045 2.00e-02 2.50e+03 pdb=" N1 DG I -33 " 0.009 2.00e-02 2.50e+03 pdb=" C2 DG I -33 " -0.036 2.00e-02 2.50e+03 pdb=" N2 DG I -33 " 0.069 2.00e-02 2.50e+03 pdb=" N3 DG I -33 " -0.070 2.00e-02 2.50e+03 pdb=" C4 DG I -33 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 47 " -0.069 2.00e-02 2.50e+03 2.63e-02 2.07e+01 pdb=" N9 DG J 47 " 0.032 2.00e-02 2.50e+03 pdb=" C8 DG J 47 " 0.025 2.00e-02 2.50e+03 pdb=" N7 DG J 47 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DG J 47 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DG J 47 " -0.012 2.00e-02 2.50e+03 pdb=" O6 DG J 47 " -0.027 2.00e-02 2.50e+03 pdb=" N1 DG J 47 " -0.010 2.00e-02 2.50e+03 pdb=" C2 DG J 47 " 0.006 2.00e-02 2.50e+03 pdb=" N2 DG J 47 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DG J 47 " 0.021 2.00e-02 2.50e+03 pdb=" C4 DG J 47 " 0.018 2.00e-02 2.50e+03 ... (remaining 1110 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1204 2.75 - 3.29: 9082 3.29 - 3.83: 19330 3.83 - 4.36: 22215 4.36 - 4.90: 32442 Nonbonded interactions: 84273 Sorted by model distance: nonbonded pdb=" O ASN D 37 " pdb=" OG SER D 38 " model vdw 2.219 3.040 nonbonded pdb=" O6 DG I 48 " pdb=" N1 DG J -49 " model vdw 2.228 3.120 nonbonded pdb=" NH2 ARG B 89 " pdb=" OD1 ASP H 56 " model vdw 2.292 3.120 nonbonded pdb=" O ASN D 37 " pdb=" OD1 ASN D 37 " model vdw 2.324 3.040 nonbonded pdb=" N ILE G 24 " pdb=" OE1 GLU G 56 " model vdw 2.331 3.120 ... (remaining 84268 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' } ncs_group { reference = (chain 'B' and resid 23 through 98) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 104) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 23 through 110) } 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.170 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 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 0.044 10511 Z= 0.377 Angle : 0.931 8.055 15184 Z= 0.586 Chirality : 0.068 0.633 1757 Planarity : 0.006 0.059 1113 Dihedral : 26.896 126.577 4452 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % 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: 1.12 (0.32), residues: 643 helix: 1.29 (0.23), residues: 495 sheet: None (None), residues: 0 loop : -1.01 (0.41), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 75 TYR 0.117 0.007 TYR B 73 PHE 0.030 0.003 PHE D 53 TRP 0.005 0.001 TRP H 25 HIS 0.004 0.001 HIS D 108 Details of bonding type rmsd covalent geometry : bond 0.00642 (10511) covalent geometry : angle 0.93085 (15184) hydrogen bonds : bond 0.11530 ( 649) hydrogen bonds : angle 4.93020 ( 1657) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.213 Fit side-chains REVERT: A 62 ASP cc_start: 0.7618 (t0) cc_final: 0.6994 (p0) REVERT: B 25 ARG cc_start: 0.7670 (ptt90) cc_final: 0.7409 (ptt-90) REVERT: B 72 GLU cc_start: 0.8449 (tp30) cc_final: 0.8015 (tp30) REVERT: C 51 MET cc_start: 0.8082 (tpp) cc_final: 0.7648 (tpt) REVERT: D 73 ARG cc_start: 0.8002 (ttm-80) cc_final: 0.7782 (ttm-80) REVERT: G 92 ASP cc_start: 0.8344 (t0) cc_final: 0.7957 (t0) REVERT: H 96 LYS cc_start: 0.7921 (tttt) cc_final: 0.7636 (tttm) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1499 time to fit residues: 21.3462 Evaluate side-chains 95 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.0870 chunk 74 optimal weight: 4.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.150381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.101609 restraints weight = 13188.266| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.11 r_work: 0.3124 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10511 Z= 0.158 Angle : 0.544 9.016 15184 Z= 0.324 Chirality : 0.031 0.126 1757 Planarity : 0.003 0.027 1113 Dihedral : 29.976 127.516 3230 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.39 % Allowed : 13.39 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.32), residues: 643 helix: 2.35 (0.22), residues: 495 sheet: None (None), residues: 0 loop : -0.81 (0.43), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 31 TYR 0.020 0.002 TYR C 57 PHE 0.022 0.002 PHE F 86 TRP 0.006 0.001 TRP H 25 HIS 0.003 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00346 (10511) covalent geometry : angle 0.54441 (15184) hydrogen bonds : bond 0.03523 ( 649) hydrogen bonds : angle 2.74228 ( 1657) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.268 Fit side-chains REVERT: A 62 ASP cc_start: 0.7522 (t0) cc_final: 0.7088 (p0) REVERT: B 25 ARG cc_start: 0.7720 (ptt90) cc_final: 0.7407 (ptt-90) REVERT: B 72 GLU cc_start: 0.8347 (tp30) cc_final: 0.8045 (tp30) REVERT: D 37 ASN cc_start: 0.8348 (t0) cc_final: 0.7975 (t0) REVERT: E 80 ASN cc_start: 0.8160 (m-40) cc_final: 0.7956 (t0) REVERT: F 73 TYR cc_start: 0.9077 (t80) cc_final: 0.8819 (t80) REVERT: F 93 LYS cc_start: 0.8417 (mtpp) cc_final: 0.8082 (mtpp) REVERT: G 92 ASP cc_start: 0.8620 (t70) cc_final: 0.8243 (t0) REVERT: H 59 GLU cc_start: 0.8517 (tp30) cc_final: 0.8310 (tp30) REVERT: H 73 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7613 (mtp85) REVERT: H 96 LYS cc_start: 0.8039 (tttt) cc_final: 0.7771 (tttm) outliers start: 13 outliers final: 8 residues processed: 101 average time/residue: 0.1183 time to fit residues: 15.4830 Evaluate side-chains 95 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 73 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 44 optimal weight: 0.0010 chunk 78 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.149906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.101037 restraints weight = 13194.114| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.14 r_work: 0.3112 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10511 Z= 0.151 Angle : 0.518 7.582 15184 Z= 0.311 Chirality : 0.030 0.115 1757 Planarity : 0.003 0.028 1113 Dihedral : 30.031 128.687 3230 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.93 % Favored : 98.91 % Rotamer: Outliers : 3.30 % Allowed : 12.11 % Favored : 84.59 % 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: 2.79 (0.32), residues: 643 helix: 2.58 (0.22), residues: 499 sheet: None (None), residues: 0 loop : -0.89 (0.43), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 67 TYR 0.018 0.001 TYR C 57 PHE 0.018 0.002 PHE H 53 TRP 0.010 0.002 TRP D 25 HIS 0.002 0.000 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00328 (10511) covalent geometry : angle 0.51821 (15184) hydrogen bonds : bond 0.03399 ( 649) hydrogen bonds : angle 2.58640 ( 1657) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.261 Fit side-chains REVERT: A 62 ASP cc_start: 0.7590 (t0) cc_final: 0.7124 (p0) REVERT: B 25 ARG cc_start: 0.7708 (ptt90) cc_final: 0.7416 (ptt-90) REVERT: B 48 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8148 (tt) REVERT: B 72 GLU cc_start: 0.8389 (tp30) cc_final: 0.7705 (tt0) REVERT: D 37 ASN cc_start: 0.8393 (t0) cc_final: 0.7934 (t0) REVERT: D 73 ARG cc_start: 0.7915 (ttm-80) cc_final: 0.7600 (ttm-80) REVERT: D 87 ARG cc_start: 0.8361 (ttm-80) cc_final: 0.7915 (ttm170) REVERT: E 80 ASN cc_start: 0.8207 (m-40) cc_final: 0.7989 (t0) REVERT: F 73 TYR cc_start: 0.9083 (t80) cc_final: 0.8814 (t80) REVERT: F 93 LYS cc_start: 0.8433 (mtpp) cc_final: 0.8091 (mtpp) REVERT: H 73 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7818 (mtp85) REVERT: H 96 LYS cc_start: 0.8066 (tttt) cc_final: 0.7809 (tttm) outliers start: 18 outliers final: 11 residues processed: 101 average time/residue: 0.1346 time to fit residues: 17.4924 Evaluate side-chains 101 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 110 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 71 optimal weight: 6.9990 chunk 27 optimal weight: 0.0040 chunk 70 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.148155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.098836 restraints weight = 13335.229| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.13 r_work: 0.3081 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10511 Z= 0.181 Angle : 0.533 7.705 15184 Z= 0.317 Chirality : 0.031 0.121 1757 Planarity : 0.003 0.024 1113 Dihedral : 30.154 129.324 3230 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.24 % Favored : 98.60 % Rotamer: Outliers : 4.04 % Allowed : 12.84 % Favored : 83.12 % 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: 2.74 (0.32), residues: 643 helix: 2.56 (0.22), residues: 499 sheet: None (None), residues: 0 loop : -0.99 (0.44), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 87 TYR 0.017 0.002 TYR C 57 PHE 0.018 0.002 PHE H 53 TRP 0.007 0.002 TRP H 25 HIS 0.004 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00410 (10511) covalent geometry : angle 0.53272 (15184) hydrogen bonds : bond 0.03581 ( 649) hydrogen bonds : angle 2.63294 ( 1657) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.157 Fit side-chains REVERT: A 62 ASP cc_start: 0.7586 (t0) cc_final: 0.7158 (p0) REVERT: A 128 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7566 (mt0) REVERT: B 25 ARG cc_start: 0.7773 (ptt90) cc_final: 0.7493 (ptt-90) REVERT: B 48 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8254 (tt) REVERT: B 72 GLU cc_start: 0.8404 (tp30) cc_final: 0.7714 (tt0) REVERT: D 37 ASN cc_start: 0.8446 (t0) cc_final: 0.7939 (t0) REVERT: D 87 ARG cc_start: 0.8415 (ttm-80) cc_final: 0.7976 (ttm170) REVERT: G 92 ASP cc_start: 0.8264 (t0) cc_final: 0.7975 (t0) REVERT: H 40 MET cc_start: 0.8316 (mmp) cc_final: 0.8066 (mmm) REVERT: H 96 LYS cc_start: 0.8082 (tttt) cc_final: 0.7815 (tttm) outliers start: 22 outliers final: 14 residues processed: 107 average time/residue: 0.1325 time to fit residues: 18.3297 Evaluate side-chains 104 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 110 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 34 optimal weight: 0.7980 chunk 7 optimal weight: 0.0060 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN H 72 ASN H 83 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.152907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.103865 restraints weight = 13348.251| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.15 r_work: 0.3157 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10511 Z= 0.137 Angle : 0.484 7.091 15184 Z= 0.294 Chirality : 0.029 0.116 1757 Planarity : 0.003 0.022 1113 Dihedral : 29.806 128.245 3230 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.09 % Favored : 98.76 % Rotamer: Outliers : 1.83 % Allowed : 16.15 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.12 (0.32), residues: 643 helix: 2.78 (0.22), residues: 504 sheet: None (None), residues: 0 loop : -0.76 (0.45), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 41 TYR 0.013 0.001 TYR C 57 PHE 0.013 0.001 PHE H 53 TRP 0.005 0.001 TRP D 25 HIS 0.001 0.000 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00293 (10511) covalent geometry : angle 0.48366 (15184) hydrogen bonds : bond 0.03291 ( 649) hydrogen bonds : angle 2.43266 ( 1657) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.156 Fit side-chains REVERT: A 62 ASP cc_start: 0.7443 (t0) cc_final: 0.7122 (p0) REVERT: B 25 ARG cc_start: 0.7727 (ptt90) cc_final: 0.7434 (ptt-90) REVERT: B 72 GLU cc_start: 0.8368 (tp30) cc_final: 0.7615 (tt0) REVERT: D 37 ASN cc_start: 0.8334 (t0) cc_final: 0.7832 (t0) REVERT: D 42 MET cc_start: 0.8178 (ptm) cc_final: 0.7905 (ptm) REVERT: D 73 ARG cc_start: 0.7925 (ttm-80) cc_final: 0.7345 (tpp-160) REVERT: D 87 ARG cc_start: 0.8239 (ttm-80) cc_final: 0.8020 (ttm170) REVERT: G 92 ASP cc_start: 0.8227 (t0) cc_final: 0.7902 (t0) REVERT: H 73 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7683 (mtp85) REVERT: H 96 LYS cc_start: 0.7949 (tttt) cc_final: 0.7662 (tttm) outliers start: 10 outliers final: 6 residues processed: 103 average time/residue: 0.1241 time to fit residues: 16.6185 Evaluate side-chains 98 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 73 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 20 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 32 optimal weight: 0.0970 chunk 49 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.150726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.102036 restraints weight = 13296.788| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.10 r_work: 0.3144 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10511 Z= 0.142 Angle : 0.489 7.079 15184 Z= 0.294 Chirality : 0.029 0.118 1757 Planarity : 0.003 0.022 1113 Dihedral : 29.822 128.974 3230 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.57 % Allowed : 15.78 % Favored : 81.65 % 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: 3.20 (0.32), residues: 643 helix: 2.82 (0.22), residues: 501 sheet: None (None), residues: 0 loop : -0.60 (0.45), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 41 TYR 0.013 0.001 TYR C 57 PHE 0.014 0.001 PHE H 53 TRP 0.007 0.001 TRP D 25 HIS 0.002 0.000 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00310 (10511) covalent geometry : angle 0.48855 (15184) hydrogen bonds : bond 0.03332 ( 649) hydrogen bonds : angle 2.43676 ( 1657) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.280 Fit side-chains REVERT: A 62 ASP cc_start: 0.7471 (t0) cc_final: 0.7195 (p0) REVERT: A 87 MET cc_start: 0.8307 (mmt) cc_final: 0.7623 (mmm) REVERT: A 128 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7467 (mt0) REVERT: B 25 ARG cc_start: 0.7680 (ptt90) cc_final: 0.7384 (ptt-90) REVERT: B 72 GLU cc_start: 0.8373 (tp30) cc_final: 0.7673 (tt0) REVERT: D 37 ASN cc_start: 0.8406 (t0) cc_final: 0.7889 (t0) REVERT: D 73 ARG cc_start: 0.7913 (ttm-80) cc_final: 0.7346 (tpp-160) REVERT: D 87 ARG cc_start: 0.8272 (ttm-80) cc_final: 0.8037 (ttm170) REVERT: D 93 ASP cc_start: 0.8299 (t70) cc_final: 0.7940 (t0) REVERT: G 68 LYS cc_start: 0.7845 (mttt) cc_final: 0.7571 (mttm) REVERT: H 73 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7723 (mtp85) REVERT: H 96 LYS cc_start: 0.8042 (tttt) cc_final: 0.7789 (tttm) outliers start: 14 outliers final: 9 residues processed: 104 average time/residue: 0.1248 time to fit residues: 17.0002 Evaluate side-chains 104 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 73 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 48 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 0.0670 chunk 69 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.151846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.102634 restraints weight = 13388.938| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.13 r_work: 0.3143 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10511 Z= 0.145 Angle : 0.488 6.955 15184 Z= 0.293 Chirality : 0.029 0.118 1757 Planarity : 0.003 0.024 1113 Dihedral : 29.788 129.023 3230 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.12 % Allowed : 16.15 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.18 (0.32), residues: 643 helix: 2.81 (0.22), residues: 501 sheet: None (None), residues: 0 loop : -0.62 (0.45), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 87 TYR 0.019 0.001 TYR B 73 PHE 0.014 0.001 PHE H 53 TRP 0.006 0.001 TRP H 25 HIS 0.002 0.000 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00316 (10511) covalent geometry : angle 0.48798 (15184) hydrogen bonds : bond 0.03335 ( 649) hydrogen bonds : angle 2.43566 ( 1657) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.209 Fit side-chains REVERT: A 62 ASP cc_start: 0.7472 (t0) cc_final: 0.7195 (p0) REVERT: A 128 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7480 (mt0) REVERT: B 25 ARG cc_start: 0.7686 (ptt90) cc_final: 0.7387 (ptt-90) REVERT: B 72 GLU cc_start: 0.8289 (tp30) cc_final: 0.7900 (tp30) REVERT: D 37 ASN cc_start: 0.8400 (t0) cc_final: 0.7878 (t0) REVERT: D 73 ARG cc_start: 0.7915 (ttm-80) cc_final: 0.7356 (tpp-160) REVERT: D 93 ASP cc_start: 0.8292 (t70) cc_final: 0.7931 (t0) REVERT: G 68 LYS cc_start: 0.7846 (mttt) cc_final: 0.7570 (mttm) REVERT: H 73 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7730 (mtp85) REVERT: H 96 LYS cc_start: 0.8035 (tttt) cc_final: 0.7752 (tttm) outliers start: 17 outliers final: 14 residues processed: 105 average time/residue: 0.1159 time to fit residues: 16.0547 Evaluate side-chains 109 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 107 PHE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 110 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 17 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.146224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.096565 restraints weight = 13323.310| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.10 r_work: 0.3054 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10511 Z= 0.222 Angle : 0.565 7.928 15184 Z= 0.330 Chirality : 0.033 0.129 1757 Planarity : 0.003 0.025 1113 Dihedral : 30.240 130.636 3230 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.71 % Favored : 98.13 % Rotamer: Outliers : 3.30 % Allowed : 17.25 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.32), residues: 643 helix: 2.41 (0.22), residues: 499 sheet: None (None), residues: 0 loop : -0.98 (0.43), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 41 TYR 0.023 0.002 TYR B 73 PHE 0.018 0.002 PHE H 53 TRP 0.010 0.002 TRP H 25 HIS 0.004 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00514 (10511) covalent geometry : angle 0.56521 (15184) hydrogen bonds : bond 0.03915 ( 649) hydrogen bonds : angle 2.74290 ( 1657) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.279 Fit side-chains REVERT: A 62 ASP cc_start: 0.7415 (t0) cc_final: 0.7106 (p0) REVERT: A 128 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7667 (mt0) REVERT: B 25 ARG cc_start: 0.7878 (ptt90) cc_final: 0.7573 (ptt-90) REVERT: B 72 GLU cc_start: 0.8283 (tp30) cc_final: 0.7825 (tp30) REVERT: D 37 ASN cc_start: 0.8457 (t0) cc_final: 0.7914 (t0) REVERT: D 87 ARG cc_start: 0.8445 (ttm170) cc_final: 0.8232 (ttp-110) REVERT: D 93 ASP cc_start: 0.8405 (t70) cc_final: 0.8021 (t0) REVERT: E 75 ARG cc_start: 0.7097 (tpp80) cc_final: 0.6447 (mtm-85) REVERT: H 23 ARG cc_start: 0.7909 (mtp85) cc_final: 0.7467 (mtp85) REVERT: H 73 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7806 (mtp85) REVERT: H 75 ARG cc_start: 0.7858 (ttm-80) cc_final: 0.7456 (ttm110) REVERT: H 96 LYS cc_start: 0.7937 (tttt) cc_final: 0.7677 (tttm) outliers start: 18 outliers final: 12 residues processed: 108 average time/residue: 0.1468 time to fit residues: 20.0868 Evaluate side-chains 108 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 110 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 20 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.150799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.101486 restraints weight = 13287.294| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.12 r_work: 0.3128 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10511 Z= 0.142 Angle : 0.497 8.051 15184 Z= 0.298 Chirality : 0.029 0.114 1757 Planarity : 0.003 0.026 1113 Dihedral : 29.839 129.234 3230 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.40 % Favored : 98.44 % Rotamer: Outliers : 2.20 % Allowed : 18.17 % Favored : 79.63 % 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: 3.02 (0.32), residues: 643 helix: 2.70 (0.22), residues: 501 sheet: None (None), residues: 0 loop : -0.67 (0.45), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 41 TYR 0.017 0.001 TYR B 73 PHE 0.013 0.001 PHE H 53 TRP 0.005 0.001 TRP H 25 HIS 0.002 0.000 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00309 (10511) covalent geometry : angle 0.49738 (15184) hydrogen bonds : bond 0.03320 ( 649) hydrogen bonds : angle 2.47845 ( 1657) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.220 Fit side-chains REVERT: A 62 ASP cc_start: 0.7413 (t0) cc_final: 0.7163 (p0) REVERT: A 128 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7558 (mt0) REVERT: B 25 ARG cc_start: 0.7852 (ptt90) cc_final: 0.7524 (ptt-90) REVERT: B 72 GLU cc_start: 0.8347 (tp30) cc_final: 0.7958 (tp30) REVERT: D 37 ASN cc_start: 0.8334 (t0) cc_final: 0.7799 (t0) REVERT: D 93 ASP cc_start: 0.8361 (t70) cc_final: 0.8015 (t0) REVERT: E 75 ARG cc_start: 0.7165 (tpp80) cc_final: 0.6477 (mtm-85) REVERT: F 73 TYR cc_start: 0.8983 (t80) cc_final: 0.8642 (t80) REVERT: H 73 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7872 (mtp85) REVERT: H 96 LYS cc_start: 0.8004 (tttt) cc_final: 0.7745 (tttm) outliers start: 12 outliers final: 10 residues processed: 100 average time/residue: 0.1371 time to fit residues: 17.6400 Evaluate side-chains 105 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 73 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 chunk 74 optimal weight: 4.9990 chunk 46 optimal weight: 0.2980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.149923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.100199 restraints weight = 13163.135| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.12 r_work: 0.3115 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10511 Z= 0.154 Angle : 0.505 8.812 15184 Z= 0.301 Chirality : 0.029 0.119 1757 Planarity : 0.003 0.025 1113 Dihedral : 29.927 129.956 3230 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.20 % Allowed : 19.27 % Favored : 78.53 % 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: 3.00 (0.32), residues: 643 helix: 2.68 (0.22), residues: 501 sheet: None (None), residues: 0 loop : -0.70 (0.45), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 36 TYR 0.019 0.001 TYR B 73 PHE 0.013 0.001 PHE H 53 TRP 0.006 0.001 TRP H 25 HIS 0.002 0.000 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00343 (10511) covalent geometry : angle 0.50501 (15184) hydrogen bonds : bond 0.03430 ( 649) hydrogen bonds : angle 2.50932 ( 1657) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.304 Fit side-chains REVERT: A 62 ASP cc_start: 0.7355 (t0) cc_final: 0.7087 (p0) REVERT: A 128 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7568 (mt0) REVERT: B 25 ARG cc_start: 0.7795 (ptt90) cc_final: 0.7465 (ptt-90) REVERT: B 72 GLU cc_start: 0.8355 (tp30) cc_final: 0.7693 (tt0) REVERT: D 37 ASN cc_start: 0.8411 (t0) cc_final: 0.7865 (t0) REVERT: D 42 MET cc_start: 0.7974 (ptm) cc_final: 0.7403 (ptm) REVERT: D 93 ASP cc_start: 0.8344 (t70) cc_final: 0.7993 (t0) REVERT: E 75 ARG cc_start: 0.7187 (tpp80) cc_final: 0.6485 (mtm-85) REVERT: H 73 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7862 (mtp85) REVERT: H 75 ARG cc_start: 0.7832 (ttm-80) cc_final: 0.7478 (ttm110) REVERT: H 96 LYS cc_start: 0.7991 (tttt) cc_final: 0.7728 (tttm) outliers start: 12 outliers final: 10 residues processed: 99 average time/residue: 0.1355 time to fit residues: 17.4226 Evaluate side-chains 104 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 73 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 61 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.150904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.101296 restraints weight = 13407.120| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.12 r_work: 0.3125 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10511 Z= 0.151 Angle : 0.501 8.688 15184 Z= 0.299 Chirality : 0.029 0.118 1757 Planarity : 0.003 0.028 1113 Dihedral : 29.878 129.965 3230 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.02 % Allowed : 19.45 % Favored : 78.53 % 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 (0.32), residues: 643 helix: 2.71 (0.22), residues: 501 sheet: None (None), residues: 0 loop : -0.69 (0.46), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 36 TYR 0.019 0.001 TYR B 73 PHE 0.013 0.001 PHE H 53 TRP 0.006 0.001 TRP H 25 HIS 0.002 0.000 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00332 (10511) covalent geometry : angle 0.50057 (15184) hydrogen bonds : bond 0.03393 ( 649) hydrogen bonds : angle 2.48977 ( 1657) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1929.88 seconds wall clock time: 33 minutes 46.63 seconds (2026.63 seconds total)