Starting phenix.real_space_refine on Thu Aug 6 00:10:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mu4_48619/08_2026/9mu4_48619.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mu4_48619/08_2026/9mu4_48619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mu4_48619/08_2026/9mu4_48619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mu4_48619/08_2026/9mu4_48619.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mu4_48619/08_2026/9mu4_48619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mu4_48619/08_2026/9mu4_48619.map" } resolution = 3.29 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= 0.006 sd= 0.039 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 328 5.49 5 S 14 5.16 5 C 7024 2.51 5 N 2384 2.21 5 O 3044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 12794 Number of models: 1 Model: "" Number of chains: 10 Chain: "c" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 812 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "g" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 812 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "d" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 753 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "h" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 753 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "a" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "e" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "b" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "f" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "T" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3344 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain breaks: 2 Chain: "N" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3380 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Time building chain proxies: 3.07, per 1000 atoms: 0.24 Number of scatterers: 12794 At special positions: 0 Unit cell: (118.841, 80.766, 159.224, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 328 15.00 O 3044 8.00 N 2384 7.00 C 7024 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: 1.05 Conformation dependent library (CDL) restraints added in 359.2 milliseconds 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1444 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 70.8% alpha, 3.1% beta 163 base pairs and 298 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'c' and resid 16 through 22 Processing helix chain 'c' and resid 26 through 36 removed outlier: 3.620A pdb=" N ILE c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.525A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 90 removed outlier: 3.575A pdb=" N ASP c 90 " --> pdb=" O ALA c 86 " (cutoff:3.500A) Processing helix chain 'c' and resid 91 through 97 Processing helix chain 'g' and resid 16 through 21 Processing helix chain 'g' and resid 26 through 36 removed outlier: 3.797A pdb=" N ILE g 30 " --> pdb=" O PRO g 26 " (cutoff:3.500A) Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.412A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 90 removed outlier: 3.576A pdb=" N LEU g 83 " --> pdb=" O ILE g 79 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP g 90 " --> pdb=" O ALA g 86 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 97 Processing helix chain 'd' and resid 35 through 47 Processing helix chain 'd' and resid 53 through 82 removed outlier: 3.668A pdb=" N ASN d 82 " --> pdb=" O LEU d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 88 through 100 removed outlier: 3.746A pdb=" N ILE d 92 " --> pdb=" O THR d 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 102 through 122 removed outlier: 3.803A pdb=" N LYS d 106 " --> pdb=" O GLY d 102 " (cutoff:3.500A) Processing helix chain 'h' and resid 35 through 47 Processing helix chain 'h' and resid 53 through 82 removed outlier: 3.566A pdb=" N ASN h 82 " --> pdb=" O LEU h 78 " (cutoff:3.500A) Processing helix chain 'h' and resid 88 through 100 removed outlier: 3.598A pdb=" N ILE h 92 " --> pdb=" O THR h 88 " (cutoff:3.500A) Processing helix chain 'h' and resid 102 through 123 removed outlier: 3.906A pdb=" N LYS h 106 " --> pdb=" O GLY h 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 45 through 56 Processing helix chain 'a' and resid 64 through 80 removed outlier: 3.545A pdb=" N PHE a 68 " --> pdb=" O ARG a 64 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP a 78 " --> pdb=" O GLU a 74 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE a 79 " --> pdb=" O ILE a 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 86 through 115 Processing helix chain 'a' and resid 121 through 132 removed outlier: 3.507A pdb=" N ILE a 125 " --> pdb=" O MET a 121 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 56 Processing helix chain 'e' and resid 64 through 80 removed outlier: 3.526A pdb=" N PHE e 68 " --> pdb=" O ARG e 64 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP e 78 " --> pdb=" O GLU e 74 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE e 79 " --> pdb=" O ILE e 75 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS e 80 " --> pdb=" O ALA e 76 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 115 Processing helix chain 'e' and resid 121 through 132 removed outlier: 3.686A pdb=" N ILE e 125 " --> pdb=" O MET e 121 " (cutoff:3.500A) Processing helix chain 'b' and resid 26 through 30 Processing helix chain 'b' and resid 31 through 43 Processing helix chain 'b' and resid 50 through 77 removed outlier: 3.966A pdb=" N GLU b 54 " --> pdb=" O LEU b 50 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG b 68 " --> pdb=" O GLU b 64 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA b 77 " --> pdb=" O TYR b 73 " (cutoff:3.500A) Processing helix chain 'b' and resid 83 through 94 removed outlier: 3.713A pdb=" N VAL b 87 " --> pdb=" O THR b 83 " (cutoff:3.500A) Processing helix chain 'f' and resid 25 through 30 removed outlier: 4.004A pdb=" N GLN f 28 " --> pdb=" O ASP f 25 " (cutoff:3.500A) Processing helix chain 'f' and resid 31 through 43 Processing helix chain 'f' and resid 50 through 77 removed outlier: 3.915A pdb=" N GLU f 54 " --> pdb=" O LEU f 50 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG f 68 " --> pdb=" O GLU f 64 " (cutoff:3.500A) Processing helix chain 'f' and resid 83 through 94 removed outlier: 3.604A pdb=" N VAL f 87 " --> pdb=" O THR f 83 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN f 94 " --> pdb=" O ALA f 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.333A pdb=" N ARG c 42 " --> pdb=" O ILE d 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AA3, first strand: chain 'c' and resid 100 through 102 Processing sheet with id=AA4, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.549A pdb=" N ARG g 42 " --> pdb=" O ILE h 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'g' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'g' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'a' and resid 84 through 85 removed outlier: 7.153A pdb=" N ARG a 84 " --> pdb=" O VAL b 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'a' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'e' and resid 84 through 85 removed outlier: 6.973A pdb=" N ARG e 84 " --> pdb=" O VAL f 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'e' and resid 119 through 120 388 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 406 hydrogen bonds 812 hydrogen bond angles 0 basepair planarities 163 basepair parallelities 298 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 1.45 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: 2495 1.33 - 1.46: 4769 1.46 - 1.58: 5748 1.58 - 1.70: 652 1.70 - 1.82: 26 Bond restraints: 13690 Sorted by residual: bond pdb=" C3' DT N -17 " pdb=" O3' DT N -17 " ideal model delta sigma weight residual 1.435 1.499 -0.064 1.30e-02 5.92e+03 2.41e+01 bond pdb=" C3' DA N 75 " pdb=" O3' DA N 75 " ideal model delta sigma weight residual 1.435 1.493 -0.058 1.30e-02 5.92e+03 1.99e+01 bond pdb=" C3' DC T 4 " pdb=" O3' DC T 4 " ideal model delta sigma weight residual 1.435 1.484 -0.049 1.30e-02 5.92e+03 1.42e+01 bond pdb=" C3' DC N -58 " pdb=" C2' DC N -58 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.37e+01 bond pdb=" C3' DA N 6 " pdb=" O3' DA N 6 " ideal model delta sigma weight residual 1.435 1.387 0.048 1.30e-02 5.92e+03 1.35e+01 ... (remaining 13685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 19143 2.34 - 4.67: 697 4.67 - 7.01: 49 7.01 - 9.35: 7 9.35 - 11.68: 4 Bond angle restraints: 19900 Sorted by residual: angle pdb=" C GLY c 37 " pdb=" N ASN c 38 " pdb=" CA ASN c 38 " ideal model delta sigma weight residual 121.54 131.40 -9.86 1.91e+00 2.74e-01 2.67e+01 angle pdb=" C3' DA N 75 " pdb=" O3' DA N 75 " pdb=" P DT N 76 " ideal model delta sigma weight residual 119.70 125.67 -5.97 1.20e+00 6.94e-01 2.48e+01 angle pdb=" C3' DT N -17 " pdb=" O3' DT N -17 " pdb=" P DT N -16 " ideal model delta sigma weight residual 119.70 125.66 -5.96 1.20e+00 6.94e-01 2.47e+01 angle pdb=" C GLY g 37 " pdb=" N ASN g 38 " pdb=" CA ASN g 38 " ideal model delta sigma weight residual 122.46 129.39 -6.93 1.41e+00 5.03e-01 2.41e+01 angle pdb=" C3' DC T 4 " pdb=" O3' DC T 4 " pdb=" P DC T 5 " ideal model delta sigma weight residual 119.70 125.29 -5.59 1.20e+00 6.94e-01 2.17e+01 ... (remaining 19895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.50: 5730 34.50 - 69.00: 1666 69.00 - 103.51: 22 103.51 - 138.01: 8 138.01 - 172.51: 2 Dihedral angle restraints: 7428 sinusoidal: 5192 harmonic: 2236 Sorted by residual: dihedral pdb=" CA ILE b 30 " pdb=" C ILE b 30 " pdb=" N THR b 31 " pdb=" CA THR b 31 " ideal model delta harmonic sigma weight residual 180.00 -155.82 -24.18 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" C4' DA N 75 " pdb=" C3' DA N 75 " pdb=" O3' DA N 75 " pdb=" P DT N 76 " ideal model delta sinusoidal sigma weight residual 220.00 47.49 172.51 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT N -17 " pdb=" C3' DT N -17 " pdb=" O3' DT N -17 " pdb=" P DT N -16 " ideal model delta sinusoidal sigma weight residual 220.00 50.33 169.67 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 7425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2003 0.081 - 0.162: 243 0.162 - 0.243: 15 0.243 - 0.324: 2 0.324 - 0.405: 1 Chirality restraints: 2264 Sorted by residual: chirality pdb=" CG LEU g 63 " pdb=" CB LEU g 63 " pdb=" CD1 LEU g 63 " pdb=" CD2 LEU g 63 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CB ILE h 52 " pdb=" CA ILE h 52 " pdb=" CG1 ILE h 52 " pdb=" CG2 ILE h 52 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE d 52 " pdb=" CA ILE d 52 " pdb=" CG1 ILE d 52 " pdb=" CG2 ILE d 52 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 2261 not shown) Planarity restraints: 1388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE g 79 " 0.048 5.00e-02 4.00e+02 7.22e-02 8.33e+00 pdb=" N PRO g 80 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO g 80 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO g 80 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET e 121 " -0.041 5.00e-02 4.00e+02 6.16e-02 6.07e+00 pdb=" N PRO e 122 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO e 122 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO e 122 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR d 119 " -0.010 2.00e-02 2.50e+03 1.61e-02 5.16e+00 pdb=" CG TYR d 119 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR d 119 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR d 119 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR d 119 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR d 119 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR d 119 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR d 119 " 0.003 2.00e-02 2.50e+03 ... (remaining 1385 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2891 2.82 - 3.34: 10658 3.34 - 3.86: 25488 3.86 - 4.38: 29416 4.38 - 4.90: 40972 Nonbonded interactions: 109425 Sorted by model distance: nonbonded pdb=" O TYR g 39 " pdb=" OG SER h 76 " model vdw 2.302 3.040 nonbonded pdb=" O TYR c 39 " pdb=" OG SER d 76 " model vdw 2.328 3.040 nonbonded pdb=" NH1 ARG c 32 " pdb=" OP1 DA T -44 " model vdw 2.354 3.120 nonbonded pdb=" NH2 ARG c 71 " pdb=" OG1 THR d 50 " model vdw 2.360 3.120 nonbonded pdb=" NE2 GLN g 24 " pdb=" OE1 GLN h 45 " model vdw 2.378 3.120 ... (remaining 109420 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' selection = chain 'f' } ncs_group { reference = chain 'c' selection = chain 'g' } ncs_group { reference = chain 'd' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.330 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.270 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 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 : 0.008 0.064 13690 Z= 0.625 Angle : 0.990 11.683 19900 Z= 0.797 Chirality : 0.054 0.405 2264 Planarity : 0.007 0.072 1388 Dihedral : 28.803 172.510 5984 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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: -1.86 (0.25), residues: 754 helix: -0.72 (0.18), residues: 536 sheet: None (None), residues: 0 loop : -2.25 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG d 77 TYR 0.039 0.003 TYR d 119 PHE 0.019 0.002 PHE c 25 HIS 0.006 0.001 HIS c 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00763 / 0.62 (13690) covalent geometry : angle 0.98958 / 0.80 (19900) hydrogen bonds : bond 0.09654 / 6.58 ( 794) hydrogen bonds : angle 3.89937 / 2.73 ( 1964) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.338 Fit side-chains REVERT: g 90 ASP cc_start: 0.8303 (t0) cc_final: 0.8009 (t0) REVERT: g 92 GLU cc_start: 0.8709 (mp0) cc_final: 0.8430 (mp0) REVERT: g 100 VAL cc_start: 0.9141 (t) cc_final: 0.8491 (t) REVERT: d 32 LYS cc_start: 0.8972 (tppt) cc_final: 0.8684 (mmmm) REVERT: d 74 GLU cc_start: 0.9133 (tp30) cc_final: 0.8933 (tp30) REVERT: h 81 TYR cc_start: 0.8667 (m-10) cc_final: 0.8439 (m-10) REVERT: h 83 LYS cc_start: 0.9349 (mptt) cc_final: 0.9078 (mttp) REVERT: h 103 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7898 (mm-30) REVERT: a 60 GLU cc_start: 0.8588 (pm20) cc_final: 0.8353 (pm20) REVERT: a 74 GLU cc_start: 0.8485 (tt0) cc_final: 0.8213 (tt0) REVERT: a 82 ASP cc_start: 0.8563 (t0) cc_final: 0.8225 (t0) REVERT: a 91 MET cc_start: 0.8948 (mpp) cc_final: 0.8577 (mmm) REVERT: a 94 GLN cc_start: 0.8962 (tt0) cc_final: 0.8668 (tt0) REVERT: a 108 THR cc_start: 0.9347 (m) cc_final: 0.9136 (t) REVERT: b 26 ASN cc_start: 0.9113 (m110) cc_final: 0.8815 (m110) REVERT: b 68 ARG cc_start: 0.8460 (ttp80) cc_final: 0.8241 (ttm170) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1537 time to fit residues: 36.5945 Evaluate side-chains 145 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 38 optimal weight: 0.0370 chunk 61 optimal weight: 0.6980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** f 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.095797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.066878 restraints weight = 40018.406| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.94 r_work: 0.3125 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13690 Z= 0.154 Angle : 0.695 8.272 19900 Z= 0.399 Chirality : 0.049 0.384 2264 Planarity : 0.005 0.050 1388 Dihedral : 31.993 175.310 4484 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.43 % Allowed : 8.44 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.29), residues: 754 helix: 1.14 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -1.96 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 35 TYR 0.030 0.002 TYR b 99 PHE 0.005 0.001 PHE c 25 HIS 0.004 0.001 HIS a 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.15 (13690) covalent geometry : angle 0.69500 / 0.40 (19900) hydrogen bonds : bond 0.04649 / 3.11 ( 794) hydrogen bonds : angle 2.85840 / 2.01 ( 1964) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 0.338 Fit side-chains REVERT: c 72 ASP cc_start: 0.8622 (t0) cc_final: 0.8005 (m-30) REVERT: d 32 LYS cc_start: 0.8785 (tppt) cc_final: 0.8465 (mmmm) REVERT: h 49 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8070 (t0) REVERT: h 81 TYR cc_start: 0.8588 (m-10) cc_final: 0.8162 (m-10) REVERT: h 83 LYS cc_start: 0.9322 (mptt) cc_final: 0.9067 (mttp) REVERT: h 103 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8111 (mm-30) REVERT: a 57 LYS cc_start: 0.9004 (ttmm) cc_final: 0.8671 (ttmt) REVERT: a 60 GLU cc_start: 0.8725 (pm20) cc_final: 0.8502 (pm20) REVERT: a 74 GLU cc_start: 0.8392 (tt0) cc_final: 0.7926 (tt0) REVERT: a 82 ASP cc_start: 0.8576 (t0) cc_final: 0.8252 (t0) REVERT: a 91 MET cc_start: 0.8734 (mpp) cc_final: 0.8385 (mmm) REVERT: b 26 ASN cc_start: 0.8952 (m110) cc_final: 0.8540 (m-40) REVERT: b 85 MET cc_start: 0.8589 (mmp) cc_final: 0.8371 (mmp) outliers start: 9 outliers final: 3 residues processed: 161 average time/residue: 0.1421 time to fit residues: 31.3303 Evaluate side-chains 145 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain h residue 49 ASP Chi-restraints excluded: chain h residue 67 ILE Chi-restraints excluded: chain a residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 96 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 0.0980 chunk 104 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 43 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 45 GLN d 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.094101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.064703 restraints weight = 40282.702| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.95 r_work: 0.3073 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13690 Z= 0.219 Angle : 0.712 8.465 19900 Z= 0.400 Chirality : 0.050 0.412 2264 Planarity : 0.005 0.046 1388 Dihedral : 32.186 177.778 4484 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.23 % Allowed : 9.87 % Favored : 87.90 % 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: 1.19 (0.30), residues: 754 helix: 1.77 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.81 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG f 93 TYR 0.024 0.002 TYR d 81 PHE 0.008 0.001 PHE c 25 HIS 0.004 0.002 HIS f 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.22 (13690) covalent geometry : angle 0.71221 / 0.40 (19900) hydrogen bonds : bond 0.05005 / 3.39 ( 794) hydrogen bonds : angle 2.74568 / 1.93 ( 1964) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.320 Fit side-chains REVERT: c 19 ASN cc_start: 0.8962 (t0) cc_final: 0.8685 (t0) REVERT: g 63 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8918 (mt) REVERT: d 32 LYS cc_start: 0.8849 (tppt) cc_final: 0.8540 (mmmm) REVERT: h 49 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8201 (t0) REVERT: h 81 TYR cc_start: 0.8726 (m-10) cc_final: 0.8325 (m-10) REVERT: h 83 LYS cc_start: 0.9315 (mptt) cc_final: 0.9058 (mttp) REVERT: a 60 GLU cc_start: 0.8771 (pm20) cc_final: 0.8539 (pm20) REVERT: a 74 GLU cc_start: 0.8491 (tt0) cc_final: 0.8276 (tt0) REVERT: a 82 ASP cc_start: 0.8610 (t0) cc_final: 0.8310 (t0) REVERT: a 88 SER cc_start: 0.9126 (p) cc_final: 0.8793 (t) REVERT: e 91 MET cc_start: 0.8862 (mmt) cc_final: 0.8641 (mmt) REVERT: b 85 MET cc_start: 0.8788 (mmp) cc_final: 0.8495 (mmp) outliers start: 14 outliers final: 11 residues processed: 155 average time/residue: 0.1279 time to fit residues: 27.4063 Evaluate side-chains 155 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain g residue 63 LEU Chi-restraints excluded: chain d residue 67 ILE Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain h residue 45 GLN Chi-restraints excluded: chain h residue 49 ASP Chi-restraints excluded: chain h residue 67 ILE Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 69 GLN Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 97 THR Chi-restraints excluded: chain f residue 50 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 7 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 45 GLN ** f 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.094405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.065033 restraints weight = 40538.923| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.95 r_work: 0.3085 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13690 Z= 0.186 Angle : 0.671 8.213 19900 Z= 0.381 Chirality : 0.048 0.401 2264 Planarity : 0.004 0.044 1388 Dihedral : 32.183 179.014 4484 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.07 % Allowed : 12.90 % Favored : 85.03 % 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: 1.60 (0.31), residues: 754 helix: 2.10 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.73 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 93 TYR 0.036 0.002 TYR b 89 PHE 0.007 0.001 PHE c 25 HIS 0.003 0.001 HIS h 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.19 (13690) covalent geometry : angle 0.67054 / 0.38 (19900) hydrogen bonds : bond 0.04363 / 2.93 ( 794) hydrogen bonds : angle 2.67876 / 1.88 ( 1964) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.331 Fit side-chains REVERT: c 19 ASN cc_start: 0.8957 (t0) cc_final: 0.8653 (t0) REVERT: c 24 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7682 (mt0) REVERT: c 72 ASP cc_start: 0.8655 (t0) cc_final: 0.7876 (m-30) REVERT: g 64 GLU cc_start: 0.8656 (tp30) cc_final: 0.8360 (tp30) REVERT: d 32 LYS cc_start: 0.8824 (tppt) cc_final: 0.8503 (mmmm) REVERT: d 45 GLN cc_start: 0.8448 (mt0) cc_final: 0.8083 (mt0) REVERT: h 49 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8208 (t0) REVERT: h 81 TYR cc_start: 0.8734 (m-10) cc_final: 0.8305 (m-10) REVERT: h 83 LYS cc_start: 0.9306 (mptt) cc_final: 0.9046 (mttp) REVERT: a 57 LYS cc_start: 0.9038 (ttmm) cc_final: 0.8732 (ttmt) REVERT: a 60 GLU cc_start: 0.8774 (pm20) cc_final: 0.8459 (pm20) REVERT: a 82 ASP cc_start: 0.8612 (t0) cc_final: 0.8318 (t0) REVERT: a 88 SER cc_start: 0.9120 (p) cc_final: 0.8780 (t) REVERT: e 91 MET cc_start: 0.8858 (mmt) cc_final: 0.8516 (mmt) outliers start: 13 outliers final: 8 residues processed: 153 average time/residue: 0.1236 time to fit residues: 26.3505 Evaluate side-chains 154 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 24 GLN Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain h residue 45 GLN Chi-restraints excluded: chain h residue 49 ASP Chi-restraints excluded: chain h residue 67 ILE Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 97 THR Chi-restraints excluded: chain f residue 50 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 83 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 78 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** f 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.094816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.065500 restraints weight = 40549.891| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.93 r_work: 0.3094 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13690 Z= 0.158 Angle : 0.649 7.910 19900 Z= 0.372 Chirality : 0.047 0.398 2264 Planarity : 0.004 0.042 1388 Dihedral : 32.085 179.727 4484 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.23 % Allowed : 13.06 % Favored : 84.71 % 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: 1.85 (0.31), residues: 754 helix: 2.29 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.66 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG f 93 TYR 0.043 0.002 TYR b 89 PHE 0.005 0.001 PHE c 25 HIS 0.002 0.001 HIS f 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 (13690) covalent geometry : angle 0.64930 / 0.37 (19900) hydrogen bonds : bond 0.04191 / 2.82 ( 794) hydrogen bonds : angle 2.63392 / 1.84 ( 1964) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.333 Fit side-chains REVERT: c 19 ASN cc_start: 0.8966 (t0) cc_final: 0.8630 (t0) REVERT: c 24 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7545 (mt0) REVERT: g 63 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8895 (mt) REVERT: d 32 LYS cc_start: 0.8801 (tppt) cc_final: 0.8488 (mmmm) REVERT: d 45 GLN cc_start: 0.8346 (mt0) cc_final: 0.7960 (mt0) REVERT: h 49 ASP cc_start: 0.8632 (m-30) cc_final: 0.8229 (t0) REVERT: h 81 TYR cc_start: 0.8767 (m-10) cc_final: 0.8321 (m-10) REVERT: h 83 LYS cc_start: 0.9280 (mptt) cc_final: 0.9014 (mttp) REVERT: a 57 LYS cc_start: 0.9035 (ttmm) cc_final: 0.8727 (ttmt) REVERT: a 60 GLU cc_start: 0.8738 (pm20) cc_final: 0.8415 (pm20) REVERT: a 82 ASP cc_start: 0.8580 (t0) cc_final: 0.8288 (t0) REVERT: a 88 SER cc_start: 0.9095 (p) cc_final: 0.8746 (t) REVERT: a 98 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7779 (mt-10) REVERT: e 91 MET cc_start: 0.8869 (mmt) cc_final: 0.8578 (mmt) outliers start: 14 outliers final: 10 residues processed: 156 average time/residue: 0.1247 time to fit residues: 26.8593 Evaluate side-chains 156 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 24 GLN Chi-restraints excluded: chain g residue 63 LEU Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain h residue 45 GLN Chi-restraints excluded: chain h residue 67 ILE Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 113 ILE Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 97 THR Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 51 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 75 optimal weight: 20.0000 chunk 95 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.091566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.061857 restraints weight = 39851.799| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.93 r_work: 0.2935 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 13690 Z= 0.370 Angle : 0.842 8.930 19900 Z= 0.448 Chirality : 0.054 0.410 2264 Planarity : 0.006 0.046 1388 Dihedral : 32.601 177.800 4484 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.87 % Allowed : 13.22 % Favored : 83.92 % 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: 1.36 (0.30), residues: 754 helix: 1.90 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -1.82 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG h 77 TYR 0.032 0.003 TYR b 89 PHE 0.024 0.002 PHE c 25 HIS 0.005 0.002 HIS f 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00789 / 0.37 (13690) covalent geometry : angle 0.84237 / 0.45 (19900) hydrogen bonds : bond 0.06207 / 4.22 ( 794) hydrogen bonds : angle 3.04001 / 2.14 ( 1964) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 19 ASN cc_start: 0.9180 (t0) cc_final: 0.8856 (t0) REVERT: c 24 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8035 (mt0) REVERT: g 64 GLU cc_start: 0.8711 (tp30) cc_final: 0.8437 (tp30) REVERT: d 32 LYS cc_start: 0.8865 (tppt) cc_final: 0.8535 (mmmm) REVERT: d 66 ASP cc_start: 0.8829 (t70) cc_final: 0.8449 (t0) REVERT: h 49 ASP cc_start: 0.8823 (m-30) cc_final: 0.8390 (t0) REVERT: h 81 TYR cc_start: 0.8969 (m-10) cc_final: 0.8408 (m-10) REVERT: h 83 LYS cc_start: 0.9384 (mptt) cc_final: 0.9107 (mttp) REVERT: a 60 GLU cc_start: 0.8752 (pm20) cc_final: 0.8358 (pm20) REVERT: a 82 ASP cc_start: 0.8728 (t0) cc_final: 0.8428 (t70) REVERT: a 88 SER cc_start: 0.9153 (p) cc_final: 0.8890 (t) REVERT: e 91 MET cc_start: 0.8983 (mmt) cc_final: 0.8778 (mmt) outliers start: 18 outliers final: 13 residues processed: 153 average time/residue: 0.1138 time to fit residues: 24.2498 Evaluate side-chains 155 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 24 GLN Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain d residue 67 ILE Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain h residue 67 ILE Chi-restraints excluded: chain a residue 74 GLU Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 113 ILE Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 87 VAL Chi-restraints excluded: chain b residue 97 THR Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 51 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 26 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 90 optimal weight: 40.0000 chunk 99 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 chunk 81 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** f 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.094102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.064530 restraints weight = 39832.090| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.78 r_work: 0.3079 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13690 Z= 0.148 Angle : 0.662 8.148 19900 Z= 0.376 Chirality : 0.047 0.393 2264 Planarity : 0.004 0.041 1388 Dihedral : 32.259 176.491 4484 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.39 % Allowed : 15.92 % Favored : 81.69 % 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: 1.90 (0.31), residues: 754 helix: 2.30 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -1.61 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG f 93 TYR 0.034 0.002 TYR b 89 PHE 0.006 0.001 PHE c 25 HIS 0.003 0.001 HIS b 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (13690) covalent geometry : angle 0.66228 / 0.38 (19900) hydrogen bonds : bond 0.04234 / 2.86 ( 794) hydrogen bonds : angle 2.68930 / 1.89 ( 1964) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: c 19 ASN cc_start: 0.8990 (t0) cc_final: 0.8662 (t0) REVERT: c 24 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7893 (mt0) REVERT: g 64 GLU cc_start: 0.8679 (tp30) cc_final: 0.8423 (tp30) REVERT: d 32 LYS cc_start: 0.8820 (tppt) cc_final: 0.8501 (mmmm) REVERT: h 49 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8270 (t0) REVERT: h 81 TYR cc_start: 0.8882 (m-10) cc_final: 0.8548 (m-10) REVERT: h 83 LYS cc_start: 0.9298 (mptt) cc_final: 0.9045 (mttp) REVERT: a 57 LYS cc_start: 0.9010 (ttmm) cc_final: 0.8770 (ttmt) REVERT: a 60 GLU cc_start: 0.8767 (pm20) cc_final: 0.8414 (pm20) REVERT: a 82 ASP cc_start: 0.8597 (t0) cc_final: 0.8298 (t0) REVERT: a 88 SER cc_start: 0.9131 (p) cc_final: 0.8813 (t) outliers start: 15 outliers final: 11 residues processed: 160 average time/residue: 0.1147 time to fit residues: 25.8288 Evaluate side-chains 156 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 24 GLN Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain h residue 45 GLN Chi-restraints excluded: chain h residue 49 ASP Chi-restraints excluded: chain h residue 67 ILE Chi-restraints excluded: chain a residue 110 LEU Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 113 ILE Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 97 THR Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 51 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 44 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 90 optimal weight: 40.0000 chunk 64 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 65 optimal weight: 0.4980 chunk 22 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** f 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.094763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.065211 restraints weight = 39814.205| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.92 r_work: 0.3093 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13690 Z= 0.145 Angle : 0.655 8.175 19900 Z= 0.371 Chirality : 0.046 0.393 2264 Planarity : 0.004 0.040 1388 Dihedral : 32.108 176.166 4484 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.55 % Allowed : 14.97 % Favored : 82.48 % 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 (0.31), residues: 754 helix: 2.42 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -1.55 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG f 93 TYR 0.031 0.002 TYR b 89 PHE 0.008 0.001 PHE c 25 HIS 0.003 0.001 HIS b 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.14 (13690) covalent geometry : angle 0.65479 / 0.37 (19900) hydrogen bonds : bond 0.04102 / 2.77 ( 794) hydrogen bonds : angle 2.61831 / 1.83 ( 1964) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.304 Fit side-chains REVERT: c 19 ASN cc_start: 0.8973 (t0) cc_final: 0.8641 (t0) REVERT: c 24 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7812 (mt0) REVERT: g 63 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8968 (mt) REVERT: g 64 GLU cc_start: 0.8676 (tp30) cc_final: 0.8391 (tp30) REVERT: d 32 LYS cc_start: 0.8815 (tppt) cc_final: 0.8494 (mmmm) REVERT: h 49 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8248 (t0) REVERT: h 81 TYR cc_start: 0.8823 (m-10) cc_final: 0.8521 (m-10) REVERT: h 83 LYS cc_start: 0.9258 (mptt) cc_final: 0.9004 (mttp) REVERT: a 57 LYS cc_start: 0.9039 (ttmm) cc_final: 0.8797 (ttmt) REVERT: a 82 ASP cc_start: 0.8559 (t0) cc_final: 0.8259 (t0) REVERT: a 88 SER cc_start: 0.9110 (p) cc_final: 0.8778 (t) REVERT: f 85 MET cc_start: 0.8880 (mmm) cc_final: 0.8391 (mmm) outliers start: 16 outliers final: 9 residues processed: 156 average time/residue: 0.1177 time to fit residues: 25.4243 Evaluate side-chains 153 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 24 GLN Chi-restraints excluded: chain g residue 63 LEU Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain h residue 45 GLN Chi-restraints excluded: chain h residue 49 ASP Chi-restraints excluded: chain h residue 67 ILE Chi-restraints excluded: chain a residue 110 LEU Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 97 THR Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 51 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 99 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 59 optimal weight: 0.0980 chunk 62 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** f 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.094623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.064867 restraints weight = 39958.720| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.78 r_work: 0.3100 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13690 Z= 0.156 Angle : 0.659 7.801 19900 Z= 0.374 Chirality : 0.046 0.388 2264 Planarity : 0.004 0.040 1388 Dihedral : 32.090 175.265 4484 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.55 % Allowed : 15.76 % Favored : 81.69 % 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: 2.09 (0.31), residues: 754 helix: 2.45 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -1.54 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG f 93 TYR 0.030 0.002 TYR b 89 PHE 0.008 0.001 PHE c 25 HIS 0.003 0.001 HIS b 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.16 (13690) covalent geometry : angle 0.65880 / 0.37 (19900) hydrogen bonds : bond 0.04100 / 2.77 ( 794) hydrogen bonds : angle 2.60462 / 1.82 ( 1964) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: c 19 ASN cc_start: 0.8966 (t0) cc_final: 0.8629 (t0) REVERT: c 24 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7799 (mt0) REVERT: d 32 LYS cc_start: 0.8792 (tppt) cc_final: 0.8478 (mmmm) REVERT: h 49 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8307 (t0) REVERT: h 81 TYR cc_start: 0.8894 (m-10) cc_final: 0.8518 (m-10) REVERT: h 83 LYS cc_start: 0.9263 (mptt) cc_final: 0.9013 (mttp) REVERT: a 57 LYS cc_start: 0.9005 (ttmm) cc_final: 0.8714 (ttmt) REVERT: a 60 GLU cc_start: 0.8684 (pm20) cc_final: 0.8405 (pm20) REVERT: a 82 ASP cc_start: 0.8546 (t0) cc_final: 0.8258 (t0) REVERT: a 88 SER cc_start: 0.9087 (p) cc_final: 0.8762 (t) outliers start: 16 outliers final: 11 residues processed: 147 average time/residue: 0.1338 time to fit residues: 27.3589 Evaluate side-chains 153 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 24 GLN Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain h residue 45 GLN Chi-restraints excluded: chain h residue 49 ASP Chi-restraints excluded: chain h residue 67 ILE Chi-restraints excluded: chain a residue 110 LEU Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 113 ILE Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 97 THR Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 4 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 93 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 0.0670 chunk 36 optimal weight: 0.9980 chunk 74 optimal weight: 50.0000 chunk 76 optimal weight: 9.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** f 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.095017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.065639 restraints weight = 40365.317| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.84 r_work: 0.3105 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13690 Z= 0.142 Angle : 0.651 10.476 19900 Z= 0.370 Chirality : 0.045 0.382 2264 Planarity : 0.004 0.039 1388 Dihedral : 32.006 174.428 4484 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.91 % Allowed : 16.56 % Favored : 81.53 % 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: 2.19 (0.31), residues: 754 helix: 2.52 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -1.52 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG f 93 TYR 0.028 0.002 TYR b 89 PHE 0.006 0.001 PHE c 25 HIS 0.002 0.001 HIS b 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.14 (13690) covalent geometry : angle 0.65090 / 0.37 (19900) hydrogen bonds : bond 0.03962 / 2.68 ( 794) hydrogen bonds : angle 2.56721 / 1.79 ( 1964) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.336 Fit side-chains REVERT: c 19 ASN cc_start: 0.8965 (t0) cc_final: 0.8624 (t0) REVERT: c 24 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7780 (mt0) REVERT: g 64 GLU cc_start: 0.8668 (tp30) cc_final: 0.8414 (tp30) REVERT: d 32 LYS cc_start: 0.8792 (tppt) cc_final: 0.8470 (mmmm) REVERT: h 49 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8319 (t0) REVERT: h 81 TYR cc_start: 0.8883 (m-10) cc_final: 0.8561 (m-10) REVERT: h 83 LYS cc_start: 0.9269 (mptt) cc_final: 0.9014 (mttp) REVERT: a 57 LYS cc_start: 0.8994 (ttmm) cc_final: 0.8705 (ttmt) REVERT: a 60 GLU cc_start: 0.8660 (pm20) cc_final: 0.8394 (pm20) REVERT: a 82 ASP cc_start: 0.8543 (t0) cc_final: 0.8247 (t0) REVERT: a 88 SER cc_start: 0.9080 (p) cc_final: 0.8753 (t) REVERT: e 91 MET cc_start: 0.8761 (mmt) cc_final: 0.8515 (mmt) outliers start: 12 outliers final: 10 residues processed: 150 average time/residue: 0.1359 time to fit residues: 28.3271 Evaluate side-chains 154 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 24 GLN Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain h residue 45 GLN Chi-restraints excluded: chain h residue 49 ASP Chi-restraints excluded: chain h residue 67 ILE Chi-restraints excluded: chain a residue 110 LEU Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 113 ILE Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 97 THR Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 60 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 75 optimal weight: 20.0000 chunk 64 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** f 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.095067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.065553 restraints weight = 40227.250| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.94 r_work: 0.3101 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13690 Z= 0.152 Angle : 0.652 7.683 19900 Z= 0.370 Chirality : 0.045 0.379 2264 Planarity : 0.004 0.040 1388 Dihedral : 32.008 173.820 4484 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.07 % Allowed : 17.04 % Favored : 80.89 % 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: 2.15 (0.31), residues: 754 helix: 2.50 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -1.53 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG f 93 TYR 0.029 0.002 TYR b 89 PHE 0.007 0.001 PHE c 25 HIS 0.005 0.001 HIS d 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (13690) covalent geometry : angle 0.65241 / 0.37 (19900) hydrogen bonds : bond 0.04030 / 2.72 ( 794) hydrogen bonds : angle 2.59396 / 1.80 ( 1964) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2796.83 seconds wall clock time: 48 minutes 30.48 seconds (2910.48 seconds total)