Starting phenix.real_space_refine on Fri Jul 3 06:00:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mu4_48619/07_2026/9mu4_48619.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mu4_48619/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9mu4_48619/07_2026/9mu4_48619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mu4_48619/07_2026/9mu4_48619.map" model { file = "/net/cci-nas-00/data/ceres_data/9mu4_48619/07_2026/9mu4_48619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mu4_48619/07_2026/9mu4_48619.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 2.30, per 1000 atoms: 0.18 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: 0.66 Conformation dependent library (CDL) restraints added in 319.0 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: 1.26 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: 2.11 Time building geometry restraints manager: 1.03 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: 19146 2.34 - 4.67: 699 4.67 - 7.01: 44 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=" 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=" N3 DT T -42 " pdb=" C4 DT T -42 " pdb=" O4 DT T -42 " ideal model delta sigma weight residual 119.90 122.66 -2.76 6.00e-01 2.78e+00 2.12e+01 angle pdb=" O5' DG T 47 " pdb=" C5' DG T 47 " pdb=" C4' DG T 47 " ideal model delta sigma weight residual 109.40 113.05 -3.65 8.00e-01 1.56e+00 2.08e+01 angle pdb=" N3 DT N -23 " pdb=" C4 DT N -23 " pdb=" O4 DT N -23 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.08e+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: 3.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.130 Find NCS groups from input model: 0.110 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.110 ------------------------------------------------------------------------------- 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= 0.624 Angle : 0.980 11.683 19900 Z= 0.786 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 0.98012 / 0.79 (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 : 0.303 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: 0.1141 time to fit residues: 27.3789 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 : 0.306 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.095755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.066793 restraints weight = 40004.563| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.94 r_work: 0.3130 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13690 Z= 0.156 Angle : 0.681 7.587 19900 Z= 0.396 Chirality : 0.049 0.364 2264 Planarity : 0.005 0.050 1388 Dihedral : 32.025 175.641 4484 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.11 % Allowed : 8.92 % Favored : 89.97 % 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: 0.41 (0.29), residues: 754 helix: 1.14 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -1.98 (0.37), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 35 TYR 0.031 0.002 TYR b 99 PHE 0.006 0.001 PHE c 25 HIS 0.003 0.001 HIS a 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.16 (13690) covalent geometry : angle 0.68099 / 0.40 (19900) hydrogen bonds : bond 0.04735 / 3.17 ( 794) hydrogen bonds : angle 2.88956 / 2.03 ( 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 164 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 157 time to evaluate : 0.219 Fit side-chains REVERT: c 72 ASP cc_start: 0.8602 (t0) cc_final: 0.7996 (m-30) REVERT: d 32 LYS cc_start: 0.8782 (tppt) cc_final: 0.8470 (mmmm) REVERT: h 81 TYR cc_start: 0.8564 (m-10) cc_final: 0.8147 (m-10) REVERT: h 83 LYS cc_start: 0.9281 (mptt) cc_final: 0.9038 (mttp) REVERT: a 57 LYS cc_start: 0.9018 (ttmm) cc_final: 0.8683 (ttmt) REVERT: a 60 GLU cc_start: 0.8725 (pm20) cc_final: 0.8514 (pm20) REVERT: a 74 GLU cc_start: 0.8385 (tt0) cc_final: 0.7929 (tt0) REVERT: a 82 ASP cc_start: 0.8558 (t0) cc_final: 0.8232 (t0) REVERT: a 91 MET cc_start: 0.8709 (mpp) cc_final: 0.8374 (mmm) REVERT: b 26 ASN cc_start: 0.8951 (m110) cc_final: 0.8576 (m-40) outliers start: 7 outliers final: 2 residues processed: 157 average time/residue: 0.1259 time to fit residues: 26.6679 Evaluate side-chains 144 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain h residue 67 ILE 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: 0.5980 chunk 104 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 43 optimal weight: 0.5980 chunk 36 optimal weight: 0.2980 chunk 86 optimal weight: 9.9990 chunk 58 optimal weight: 0.0970 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 45 GLN d 82 ASN a 94 GLN ** f 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.094927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.065779 restraints weight = 40269.063| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.97 r_work: 0.3102 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1223 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= 0.178 Angle : 0.658 7.745 19900 Z= 0.382 Chirality : 0.047 0.372 2264 Planarity : 0.005 0.044 1388 Dihedral : 32.130 178.169 4484 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.07 % Allowed : 9.39 % Favored : 88.54 % 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: 1.31 (0.30), residues: 754 helix: 1.86 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.78 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG c 35 TYR 0.025 0.002 TYR b 89 PHE 0.006 0.001 PHE a 68 HIS 0.006 0.001 HIS h 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.18 (13690) covalent geometry : angle 0.65753 / 0.38 (19900) hydrogen bonds : bond 0.04496 / 3.03 ( 794) hydrogen bonds : angle 2.68916 / 1.89 ( 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 160 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.306 Fit side-chains REVERT: c 19 ASN cc_start: 0.8946 (t0) cc_final: 0.8667 (t0) REVERT: c 56 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8809 (tm-30) REVERT: c 71 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7367 (mmt-90) REVERT: c 72 ASP cc_start: 0.8545 (t0) cc_final: 0.7943 (m-30) REVERT: d 32 LYS cc_start: 0.8836 (tppt) cc_final: 0.8534 (mmmm) REVERT: h 49 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8054 (t0) REVERT: h 81 TYR cc_start: 0.8685 (m-10) cc_final: 0.8316 (m-10) REVERT: h 83 LYS cc_start: 0.9329 (mptt) cc_final: 0.9078 (mttp) REVERT: a 57 LYS cc_start: 0.9020 (ttmm) cc_final: 0.8696 (ttmt) REVERT: a 60 GLU cc_start: 0.8724 (pm20) cc_final: 0.8503 (pm20) REVERT: a 74 GLU cc_start: 0.8449 (tt0) cc_final: 0.8091 (tt0) REVERT: a 82 ASP cc_start: 0.8581 (t0) cc_final: 0.8277 (t0) REVERT: e 91 MET cc_start: 0.8815 (mmt) cc_final: 0.8575 (mmt) REVERT: b 26 ASN cc_start: 0.8983 (m110) cc_final: 0.8618 (m110) REVERT: b 89 TYR cc_start: 0.8378 (m-80) cc_final: 0.7954 (m-80) outliers start: 13 outliers final: 8 residues processed: 152 average time/residue: 0.1046 time to fit residues: 22.1501 Evaluate side-chains 149 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 71 ARG 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 7 optimal weight: 0.6980 chunk 78 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 73 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 93 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3919 r_free = 0.3919 target = 0.094603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.065186 restraints weight = 40243.497| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.81 r_work: 0.3032 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1419 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= 0.181 Angle : 0.646 7.665 19900 Z= 0.373 Chirality : 0.046 0.369 2264 Planarity : 0.004 0.043 1388 Dihedral : 32.197 179.126 4484 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.23 % Allowed : 11.94 % Favored : 85.83 % 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 (0.30), residues: 754 helix: 2.08 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.67 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 93 TYR 0.024 0.002 TYR d 81 PHE 0.007 0.001 PHE g 25 HIS 0.003 0.001 HIS f 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.18 (13690) covalent geometry : angle 0.64610 / 0.37 (19900) hydrogen bonds : bond 0.04342 / 2.91 ( 794) hydrogen bonds : angle 2.64150 / 1.86 ( 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 163 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.294 Fit side-chains REVERT: c 19 ASN cc_start: 0.9001 (t0) cc_final: 0.8683 (t0) REVERT: c 24 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7688 (mt0) REVERT: c 72 ASP cc_start: 0.8655 (t0) cc_final: 0.7973 (m-30) REVERT: g 64 GLU cc_start: 0.8689 (tp30) cc_final: 0.8412 (tp30) REVERT: d 32 LYS cc_start: 0.8826 (tppt) cc_final: 0.8502 (mmmm) REVERT: d 45 GLN cc_start: 0.8415 (mt0) cc_final: 0.8056 (mt0) REVERT: h 49 ASP cc_start: 0.8784 (OUTLIER) cc_final: 0.8164 (t0) REVERT: h 81 TYR cc_start: 0.8758 (m-10) cc_final: 0.8330 (m-10) REVERT: h 83 LYS cc_start: 0.9348 (mptt) cc_final: 0.9074 (mttp) REVERT: a 57 LYS cc_start: 0.9011 (ttmm) cc_final: 0.8681 (ttmt) REVERT: a 60 GLU cc_start: 0.8740 (pm20) cc_final: 0.8377 (pm20) REVERT: a 82 ASP cc_start: 0.8703 (t0) cc_final: 0.8392 (t0) REVERT: a 88 SER cc_start: 0.9098 (p) cc_final: 0.8749 (t) REVERT: a 98 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7606 (mt-10) REVERT: e 91 MET cc_start: 0.8901 (mmt) cc_final: 0.8564 (mmt) REVERT: b 89 TYR cc_start: 0.8497 (m-10) cc_final: 0.7998 (m-80) outliers start: 14 outliers final: 10 residues processed: 156 average time/residue: 0.1139 time to fit residues: 24.4349 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 : 0.277 ------------------------------------------------------------------------------- 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 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 87 VAL 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: 0.5980 chunk 47 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 52 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.094798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.065470 restraints weight = 40172.580| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.84 r_work: 0.3102 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13690 Z= 0.162 Angle : 0.635 7.476 19900 Z= 0.368 Chirality : 0.046 0.365 2264 Planarity : 0.004 0.042 1388 Dihedral : 32.162 179.767 4484 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.39 % Allowed : 12.58 % 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: 1.75 (0.31), residues: 754 helix: 2.19 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -1.66 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG f 93 TYR 0.011 0.001 TYR g 57 PHE 0.005 0.001 PHE g 25 HIS 0.002 0.001 HIS f 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 (13690) covalent geometry : angle 0.63505 / 0.37 (19900) hydrogen bonds : bond 0.04191 / 2.82 ( 794) hydrogen bonds : angle 2.63973 / 1.86 ( 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 165 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.277 Fit side-chains REVERT: c 19 ASN cc_start: 0.8946 (t0) cc_final: 0.8614 (t0) REVERT: c 24 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7427 (mt0) REVERT: c 72 ASP cc_start: 0.8595 (t0) cc_final: 0.8001 (m-30) REVERT: g 64 GLU cc_start: 0.8676 (tp30) cc_final: 0.8372 (tp30) REVERT: d 32 LYS cc_start: 0.8796 (tppt) cc_final: 0.8488 (mmmm) REVERT: d 45 GLN cc_start: 0.8315 (mt0) cc_final: 0.7937 (mt0) REVERT: h 38 TYR cc_start: 0.8932 (m-80) cc_final: 0.8605 (m-80) REVERT: h 49 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8108 (t0) REVERT: h 81 TYR cc_start: 0.8721 (m-10) cc_final: 0.8275 (m-10) REVERT: h 83 LYS cc_start: 0.9268 (mptt) cc_final: 0.9006 (mttp) REVERT: a 57 LYS cc_start: 0.9017 (ttmm) cc_final: 0.8710 (ttmt) REVERT: a 60 GLU cc_start: 0.8726 (pm20) cc_final: 0.8445 (pm20) REVERT: a 82 ASP cc_start: 0.8579 (t0) cc_final: 0.8285 (t0) REVERT: a 88 SER cc_start: 0.9091 (p) cc_final: 0.8732 (t) REVERT: e 91 MET cc_start: 0.8843 (mmt) cc_final: 0.8565 (mmt) REVERT: b 26 ASN cc_start: 0.8987 (m110) cc_final: 0.8776 (m-40) outliers start: 15 outliers final: 9 residues processed: 158 average time/residue: 0.1092 time to fit residues: 24.0723 Evaluate side-chains 156 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 75 optimal weight: 20.0000 chunk 95 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 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: 0.5980 chunk 14 optimal weight: 0.9990 chunk 73 optimal weight: 0.1980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.092870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.063060 restraints weight = 40093.176| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.99 r_work: 0.3034 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13690 Z= 0.290 Angle : 0.747 8.133 19900 Z= 0.411 Chirality : 0.050 0.375 2264 Planarity : 0.005 0.045 1388 Dihedral : 32.513 178.604 4484 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.03 % Allowed : 13.54 % Favored : 83.44 % 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: 1.49 (0.30), residues: 754 helix: 1.99 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -1.74 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG h 77 TYR 0.020 0.002 TYR b 89 PHE 0.017 0.002 PHE c 25 HIS 0.005 0.002 HIS b 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.29 (13690) covalent geometry : angle 0.74732 / 0.41 (19900) hydrogen bonds : bond 0.05460 / 3.70 ( 794) hydrogen bonds : angle 2.86373 / 2.03 ( 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 167 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: c 19 ASN cc_start: 0.9031 (t0) cc_final: 0.8701 (t0) REVERT: c 24 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.7948 (mt0) REVERT: c 61 GLU cc_start: 0.8170 (tp30) cc_final: 0.7669 (tp30) REVERT: c 71 ARG cc_start: 0.7712 (tpp80) cc_final: 0.7416 (mtt90) REVERT: d 32 LYS cc_start: 0.8805 (tppt) cc_final: 0.8488 (mmmm) REVERT: d 66 ASP cc_start: 0.8721 (t70) cc_final: 0.8363 (t0) REVERT: h 49 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8173 (t0) REVERT: h 81 TYR cc_start: 0.8855 (m-10) cc_final: 0.8374 (m-10) REVERT: h 83 LYS cc_start: 0.9290 (mptt) cc_final: 0.9024 (mttp) REVERT: h 91 GLU cc_start: 0.8386 (mp0) cc_final: 0.8177 (mp0) REVERT: h 103 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7854 (mm-30) REVERT: a 57 LYS cc_start: 0.9061 (ttmm) cc_final: 0.8798 (ttmt) REVERT: a 60 GLU cc_start: 0.8833 (pm20) cc_final: 0.8452 (pm20) REVERT: a 82 ASP cc_start: 0.8624 (t0) cc_final: 0.8339 (t70) REVERT: a 88 SER cc_start: 0.9153 (p) cc_final: 0.8843 (t) REVERT: e 60 GLU cc_start: 0.8317 (pm20) cc_final: 0.7969 (pm20) outliers start: 19 outliers final: 13 residues processed: 157 average time/residue: 0.1153 time to fit residues: 24.8779 Evaluate side-chains 159 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 45 GLN Chi-restraints excluded: chain h residue 49 ASP 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 69 GLN 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 26 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 90 optimal weight: 40.0000 chunk 99 optimal weight: 7.9990 chunk 1 optimal weight: 0.5980 chunk 81 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.094418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.064904 restraints weight = 39855.127| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.74 r_work: 0.3090 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13690 Z= 0.150 Angle : 0.643 7.545 19900 Z= 0.369 Chirality : 0.046 0.361 2264 Planarity : 0.004 0.042 1388 Dihedral : 32.288 177.660 4484 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.55 % Allowed : 14.65 % Favored : 82.80 % 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: 1.83 (0.31), residues: 754 helix: 2.24 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.57 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG f 93 TYR 0.014 0.002 TYR d 81 PHE 0.007 0.001 PHE c 25 HIS 0.002 0.001 HIS h 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (13690) covalent geometry : angle 0.64329 / 0.37 (19900) hydrogen bonds : bond 0.04194 / 2.82 ( 794) hydrogen bonds : angle 2.67376 / 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 167 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: c 19 ASN cc_start: 0.8983 (t0) cc_final: 0.8642 (t0) REVERT: c 24 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.7876 (mt0) REVERT: c 71 ARG cc_start: 0.7692 (tpp80) cc_final: 0.7372 (mtt90) REVERT: c 72 ASP cc_start: 0.8664 (t0) cc_final: 0.7899 (m-30) REVERT: d 32 LYS cc_start: 0.8776 (tppt) cc_final: 0.8457 (mmmm) REVERT: h 38 TYR cc_start: 0.8905 (m-80) cc_final: 0.8572 (m-80) REVERT: h 49 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.8130 (t0) REVERT: h 81 TYR cc_start: 0.8810 (m-10) cc_final: 0.8460 (m-10) REVERT: h 83 LYS cc_start: 0.9269 (mptt) cc_final: 0.9014 (mttp) REVERT: a 57 LYS cc_start: 0.8993 (ttmm) cc_final: 0.8680 (ttmt) REVERT: a 60 GLU cc_start: 0.8742 (pm20) cc_final: 0.8358 (pm20) REVERT: a 82 ASP cc_start: 0.8585 (t0) cc_final: 0.8283 (t0) REVERT: a 88 SER cc_start: 0.9110 (p) cc_final: 0.8748 (t) REVERT: a 98 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7706 (mt-10) outliers start: 16 outliers final: 10 residues processed: 157 average time/residue: 0.1142 time to fit residues: 25.0074 Evaluate side-chains 155 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- 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: 0.7980 chunk 51 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 22 optimal weight: 0.0170 chunk 47 optimal weight: 0.3980 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.095275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.067056 restraints weight = 39477.945| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.94 r_work: 0.3107 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13690 Z= 0.139 Angle : 0.621 7.191 19900 Z= 0.361 Chirality : 0.045 0.361 2264 Planarity : 0.004 0.041 1388 Dihedral : 32.095 177.214 4484 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.07 % Allowed : 14.81 % 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: 2.03 (0.31), residues: 754 helix: 2.36 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -1.44 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG f 93 TYR 0.011 0.001 TYR d 81 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 0.00242 / 0.14 (13690) covalent geometry : angle 0.62072 / 0.36 (19900) hydrogen bonds : bond 0.03967 / 2.66 ( 794) hydrogen bonds : angle 2.58789 / 1.82 ( 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 161 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: c 19 ASN cc_start: 0.8980 (t0) cc_final: 0.8630 (t0) REVERT: c 24 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7788 (mt0) REVERT: c 71 ARG cc_start: 0.7709 (tpp80) cc_final: 0.7373 (mtt90) REVERT: d 32 LYS cc_start: 0.8796 (tppt) cc_final: 0.8480 (mmmm) REVERT: h 38 TYR cc_start: 0.8907 (m-80) cc_final: 0.8544 (m-80) REVERT: h 49 ASP cc_start: 0.8687 (t70) cc_final: 0.8123 (t0) REVERT: h 81 TYR cc_start: 0.8794 (m-10) cc_final: 0.7902 (m-10) REVERT: h 83 LYS cc_start: 0.9280 (mptt) cc_final: 0.9031 (mttp) REVERT: a 57 LYS cc_start: 0.9006 (ttmm) cc_final: 0.8694 (ttmt) REVERT: a 82 ASP cc_start: 0.8600 (t0) cc_final: 0.8301 (t0) REVERT: a 88 SER cc_start: 0.9072 (p) cc_final: 0.8742 (t) REVERT: a 98 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7606 (mt-10) REVERT: e 51 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8434 (mt-10) REVERT: b 89 TYR cc_start: 0.8021 (m-10) cc_final: 0.7268 (m-10) REVERT: f 89 TYR cc_start: 0.9082 (m-10) cc_final: 0.8163 (m-80) outliers start: 13 outliers final: 8 residues processed: 154 average time/residue: 0.1152 time to fit residues: 24.6663 Evaluate side-chains 152 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 67 ILE 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: 0.6980 chunk 2 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.094858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.065227 restraints weight = 40001.075| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.79 r_work: 0.3108 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13690 Z= 0.168 Angle : 0.651 10.744 19900 Z= 0.372 Chirality : 0.045 0.360 2264 Planarity : 0.004 0.040 1388 Dihedral : 32.145 176.610 4484 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.91 % Allowed : 15.61 % 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: 2.41 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.46 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG f 93 TYR 0.019 0.002 TYR d 81 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 0.00324 / 0.17 (13690) covalent geometry : angle 0.65142 / 0.37 (19900) hydrogen bonds : bond 0.04126 / 2.78 ( 794) hydrogen bonds : angle 2.65197 / 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 153 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: c 19 ASN cc_start: 0.8972 (t0) cc_final: 0.8622 (t0) REVERT: c 24 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7810 (mt0) REVERT: c 71 ARG cc_start: 0.7744 (tpp80) cc_final: 0.7381 (mtt90) REVERT: d 32 LYS cc_start: 0.8778 (tppt) cc_final: 0.8463 (mmmm) REVERT: h 49 ASP cc_start: 0.8707 (t70) cc_final: 0.8152 (t0) REVERT: h 81 TYR cc_start: 0.8876 (m-10) cc_final: 0.7951 (m-10) REVERT: h 83 LYS cc_start: 0.9248 (mptt) cc_final: 0.8992 (mttp) REVERT: a 57 LYS cc_start: 0.9033 (ttmm) cc_final: 0.8739 (ttmt) REVERT: a 60 GLU cc_start: 0.8707 (pm20) cc_final: 0.8422 (pm20) REVERT: a 61 LEU cc_start: 0.8671 (tp) cc_final: 0.8372 (tp) REVERT: a 82 ASP cc_start: 0.8580 (t0) cc_final: 0.8290 (t0) REVERT: a 88 SER cc_start: 0.9099 (p) cc_final: 0.8761 (t) REVERT: a 98 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7545 (mt-10) REVERT: e 51 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8417 (mt-10) REVERT: f 85 MET cc_start: 0.8900 (mmm) cc_final: 0.8405 (mmm) REVERT: f 89 TYR cc_start: 0.9051 (m-10) cc_final: 0.7953 (m-80) outliers start: 12 outliers final: 10 residues processed: 146 average time/residue: 0.1127 time to fit residues: 22.9173 Evaluate side-chains 151 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 24 GLN Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain d residue 81 TYR 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 b residue 31 THR Chi-restraints excluded: chain b residue 87 VAL Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain b residue 97 THR Chi-restraints excluded: chain f residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 4 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 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: 0.7980 chunk 36 optimal weight: 0.6980 chunk 74 optimal weight: 40.0000 chunk 76 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 82 ASN ** 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 = 0.3930 r_free = 0.3930 target = 0.095143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.065765 restraints weight = 40209.076| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.94 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: 0.8789 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13690 Z= 0.154 Angle : 0.636 8.245 19900 Z= 0.366 Chirality : 0.044 0.355 2264 Planarity : 0.004 0.040 1388 Dihedral : 32.115 175.615 4484 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.23 % Allowed : 15.76 % Favored : 82.01 % 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: 2.13 (0.31), residues: 754 helix: 2.46 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.43 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG f 93 TYR 0.033 0.002 TYR b 89 PHE 0.007 0.001 PHE c 25 HIS 0.002 0.001 HIS f 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 (13690) covalent geometry : angle 0.63636 / 0.37 (19900) hydrogen bonds : bond 0.04009 / 2.71 ( 794) hydrogen bonds : angle 2.62396 / 1.80 ( 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: 14 poor density : 144 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 19 ASN cc_start: 0.8984 (t0) cc_final: 0.8633 (t0) REVERT: c 24 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7809 (mt0) REVERT: c 71 ARG cc_start: 0.7756 (tpp80) cc_final: 0.7361 (mtt90) REVERT: g 64 GLU cc_start: 0.8693 (tp30) cc_final: 0.8338 (tp30) REVERT: d 32 LYS cc_start: 0.8782 (tppt) cc_final: 0.8453 (mmmm) REVERT: h 49 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8206 (t0) REVERT: h 81 TYR cc_start: 0.8895 (m-10) cc_final: 0.8567 (m-10) REVERT: h 83 LYS cc_start: 0.9282 (mptt) cc_final: 0.9020 (mttp) REVERT: a 57 LYS cc_start: 0.8988 (ttmm) cc_final: 0.8699 (ttmt) REVERT: a 60 GLU cc_start: 0.8723 (pm20) cc_final: 0.8426 (pm20) REVERT: a 82 ASP cc_start: 0.8586 (t0) cc_final: 0.8289 (t0) REVERT: a 88 SER cc_start: 0.9089 (p) cc_final: 0.8763 (t) REVERT: a 98 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7519 (mt-10) REVERT: e 51 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8423 (mt-10) REVERT: f 85 MET cc_start: 0.8996 (mmm) cc_final: 0.8441 (mmm) outliers start: 14 outliers final: 11 residues processed: 149 average time/residue: 0.1178 time to fit residues: 24.4446 Evaluate side-chains 152 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 24 GLN Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain d residue 81 TYR 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 87 VAL Chi-restraints excluded: chain b residue 88 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 60 optimal weight: 0.3980 chunk 56 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 64 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 87 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.095237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.066051 restraints weight = 39748.114| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.93 r_work: 0.3110 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13690 Z= 0.152 Angle : 0.639 8.983 19900 Z= 0.366 Chirality : 0.044 0.352 2264 Planarity : 0.004 0.040 1388 Dihedral : 32.090 174.942 4484 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.07 % Allowed : 16.08 % Favored : 81.85 % 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: 2.17 (0.31), residues: 754 helix: 2.49 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.43 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG f 93 TYR 0.049 0.002 TYR b 89 PHE 0.007 0.001 PHE c 25 HIS 0.002 0.001 HIS b 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (13690) covalent geometry : angle 0.63929 / 0.37 (19900) hydrogen bonds : bond 0.04019 / 2.71 ( 794) hydrogen bonds : angle 2.62998 / 1.80 ( 1964) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2551.30 seconds wall clock time: 44 minutes 17.60 seconds (2657.60 seconds total)