Starting phenix.real_space_refine on Fri Jul 3 08:52:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pep_17634/07_2026/8pep_17634.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pep_17634/07_2026/8pep_17634.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pep_17634/07_2026/8pep_17634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pep_17634/07_2026/8pep_17634.map" model { file = "/net/cci-nas-00/data/ceres_data/8pep_17634/07_2026/8pep_17634.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pep_17634/07_2026/8pep_17634.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8pep_17634/07_2026/8pep_17634.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pep_17634/07_2026/8pep_17634.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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 293 5.49 5 S 15 5.16 5 C 7599 2.51 5 N 2518 2.21 5 O 3067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s 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: 13492 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 827 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Planarities with less than four sites: {'M2L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 656 Classifications: {'peptide': 82} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 692 Classifications: {'peptide': 86} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2971 Inner-chain residues flagged as termini: ['pdbres=" DT I -72 "'] Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen planarities: 22 Chain: "K" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 708 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "J" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3014 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen planarities: 17 Chain: "L" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 710 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Time building chain proxies: 2.64, per 1000 atoms: 0.20 Number of scatterers: 13492 At special positions: 0 Unit cell: (95.019, 120.024, 138.361, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 293 15.00 O 3067 8.00 N 2518 7.00 C 7599 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: 1.04 Conformation dependent library (CDL) restraints added in 429.6 milliseconds 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1756 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 12 sheets defined 59.6% alpha, 6.2% beta 135 base pairs and 265 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.532A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.613A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.890A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.551A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.892A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.571A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.976A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.249A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.853A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.565A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.330A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 4.263A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 83 Processing helix chain 'L' and resid 76 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.660A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.407A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.251A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.411A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.331A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 49 through 53 removed outlier: 4.040A pdb=" N GLU K 49 " --> pdb=" O PHE K 44 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 49 through 53 removed outlier: 3.984A pdb=" N GLU L 49 " --> pdb=" O PHE L 44 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA L 51 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE L 42 " --> pdb=" O ALA L 51 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 342 hydrogen bonds 680 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 265 stacking parallelities Total time for adding SS restraints: 2.67 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: 1.22 - 1.34: 3179 1.34 - 1.46: 4341 1.46 - 1.58: 6223 1.58 - 1.70: 584 1.70 - 1.82: 30 Bond restraints: 14357 Sorted by residual: bond pdb=" C3' DC J -71 " pdb=" C2' DC J -71 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.63e+01 bond pdb=" C3' DC I 33 " pdb=" C2' DC I 33 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.47e+01 bond pdb=" C3' DC I -18 " pdb=" C2' DC I -18 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.38e+01 bond pdb=" C3' DC I 21 " pdb=" C2' DC I 21 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.29e+01 bond pdb=" C3' DT J -59 " pdb=" C2' DT J -59 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 ... (remaining 14352 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 20325 2.72 - 5.44: 278 5.44 - 8.16: 11 8.16 - 10.88: 3 10.88 - 13.60: 2 Bond angle restraints: 20619 Sorted by residual: angle pdb=" CB LYS K 65 " pdb=" CG LYS K 65 " pdb=" CD LYS K 65 " ideal model delta sigma weight residual 111.30 124.90 -13.60 2.30e+00 1.89e-01 3.50e+01 angle pdb=" CA LYS K 65 " pdb=" CB LYS K 65 " pdb=" CG LYS K 65 " ideal model delta sigma weight residual 114.10 125.68 -11.58 2.00e+00 2.50e-01 3.35e+01 angle pdb=" O4' DA J 16 " pdb=" C1' DA J 16 " pdb=" N9 DA J 16 " ideal model delta sigma weight residual 108.00 111.69 -3.69 7.00e-01 2.04e+00 2.77e+01 angle pdb=" O5' DA I 67 " pdb=" C5' DA I 67 " pdb=" C4' DA I 67 " ideal model delta sigma weight residual 109.40 113.42 -4.02 8.00e-01 1.56e+00 2.53e+01 angle pdb=" O4' DT J -72 " pdb=" C1' DT J -72 " pdb=" N1 DT J -72 " ideal model delta sigma weight residual 108.00 111.29 -3.29 7.00e-01 2.04e+00 2.21e+01 ... (remaining 20614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 6267 35.32 - 70.63: 1598 70.63 - 105.95: 41 105.95 - 141.26: 3 141.26 - 176.58: 4 Dihedral angle restraints: 7913 sinusoidal: 5194 harmonic: 2719 Sorted by residual: dihedral pdb=" CD M2L A 36 " pdb=" CE M2L A 36 " pdb=" NZ M2L A 36 " pdb=" CM1 M2L A 36 " ideal model delta sinusoidal sigma weight residual 66.23 -97.70 163.93 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C4' DT J 69 " pdb=" C3' DT J 69 " pdb=" O3' DT J 69 " pdb=" P DC J 70 " ideal model delta sinusoidal sigma weight residual 220.00 43.42 176.58 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC J 68 " pdb=" C3' DC J 68 " pdb=" O3' DC J 68 " pdb=" P DT J 69 " ideal model delta sinusoidal sigma weight residual -140.00 24.58 -164.58 1 3.50e+01 8.16e-04 1.54e+01 ... (remaining 7910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1865 0.061 - 0.123: 410 0.123 - 0.184: 40 0.184 - 0.245: 5 0.245 - 0.307: 2 Chirality restraints: 2322 Sorted by residual: chirality pdb=" CB ILE L 58 " pdb=" CA ILE L 58 " pdb=" CG1 ILE L 58 " pdb=" CG2 ILE L 58 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA LYS K 65 " pdb=" N LYS K 65 " pdb=" C LYS K 65 " pdb=" CB LYS K 65 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA ASP F 24 " pdb=" N ASP F 24 " pdb=" C ASP F 24 " pdb=" CB ASP F 24 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 2319 not shown) Planarity restraints: 1605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 23 " -0.017 2.00e-02 2.50e+03 3.50e-02 1.23e+01 pdb=" C ARG F 23 " 0.061 2.00e-02 2.50e+03 pdb=" O ARG F 23 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP F 24 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 114 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C ALA D 114 " 0.058 2.00e-02 2.50e+03 pdb=" O ALA D 114 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL D 115 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 55 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C ARG F 55 " 0.057 2.00e-02 2.50e+03 pdb=" O ARG F 55 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY F 56 " -0.019 2.00e-02 2.50e+03 ... (remaining 1602 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 246 2.65 - 3.22: 11181 3.22 - 3.78: 24818 3.78 - 4.34: 32052 4.34 - 4.90: 46603 Nonbonded interactions: 114900 Sorted by model distance: nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.092 3.040 nonbonded pdb=" O PRO K 60 " pdb=" ND2 ASN K 64 " model vdw 2.100 3.120 nonbonded pdb=" O GLU K 66 " pdb=" NZ LYS K 70 " model vdw 2.222 3.120 nonbonded pdb=" OG1 THR A 118 " pdb=" NH1 ARG B 45 " model vdw 2.235 3.120 nonbonded pdb=" OE1 GLU A 73 " pdb=" ND2 ASN B 25 " model vdw 2.244 3.120 ... (remaining 114895 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and (resid 20 through 100 or (resid 101 and (name N or name CA or nam \ e C )))) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = (chain 'L' and (resid 1 through 28 or (resid 29 and (name N or name CA or name C \ or name CB or name CG or name CD )) or resid 35 through 90 or (resid 91 and (na \ me N or name CA or name C or name CB or name CG or name CD or name CE or name NZ \ )))) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.980 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 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 : 0.005 0.039 14357 Z= 0.482 Angle : 0.855 13.598 20619 Z= 0.719 Chirality : 0.050 0.307 2322 Planarity : 0.007 0.086 1605 Dihedral : 28.764 176.578 6157 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.13 % Allowed : 3.04 % Favored : 96.83 % 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: 0.85 (0.27), residues: 913 helix: 1.74 (0.22), residues: 548 sheet: -2.95 (0.69), residues: 34 loop : -1.06 (0.30), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG E 129 TYR 0.035 0.002 TYR K 61 PHE 0.036 0.002 PHE C 25 TRP 0.008 0.001 TRP K 21 HIS 0.007 0.001 HIS L 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.48 (14357) covalent geometry : angle 0.85518 / 0.72 (20619) hydrogen bonds : bond 0.19360 / 13.44 ( 771) hydrogen bonds : angle 6.29768 / 4.50 ( 1940) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: E 56 LYS cc_start: 0.8835 (mtpp) cc_final: 0.8596 (mtmm) REVERT: G 38 ASN cc_start: 0.7909 (m-40) cc_final: 0.7454 (m-40) REVERT: K 52 PHE cc_start: 0.8284 (m-10) cc_final: 0.8077 (m-80) REVERT: K 78 ASN cc_start: 0.9218 (m-40) cc_final: 0.8985 (m-40) REVERT: L 20 HIS cc_start: 0.7653 (m-70) cc_final: 0.7016 (m170) REVERT: L 59 PHE cc_start: 0.8454 (m-80) cc_final: 0.7894 (m-80) REVERT: L 77 PHE cc_start: 0.8300 (t80) cc_final: 0.7713 (t80) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.1676 time to fit residues: 34.3646 Evaluate side-chains 85 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 0.0270 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 30.0000 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 46 HIS D 81 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.063365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.041629 restraints weight = 65112.832| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 2.88 r_work: 0.2620 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14357 Z= 0.162 Angle : 0.700 9.139 20619 Z= 0.393 Chirality : 0.048 0.323 2322 Planarity : 0.005 0.039 1605 Dihedral : 32.095 178.379 4250 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.64 % Favored : 98.25 % Rotamer: Outliers : 0.51 % Allowed : 7.98 % Favored : 91.51 % 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: 1.25 (0.28), residues: 913 helix: 2.07 (0.22), residues: 563 sheet: -2.51 (1.01), residues: 22 loop : -1.19 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 74 TYR 0.023 0.002 TYR L 61 PHE 0.021 0.002 PHE L 5 TRP 0.017 0.003 TRP L 82 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.16 (14357) covalent geometry : angle 0.69967 / 0.39 (20619) hydrogen bonds : bond 0.05523 / 3.83 ( 771) hydrogen bonds : angle 3.58354 / 2.47 ( 1940) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7399 (t-90) cc_final: 0.7136 (t-90) REVERT: C 92 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8003 (mt-10) REVERT: D 32 GLU cc_start: 0.8874 (pm20) cc_final: 0.8646 (pm20) REVERT: D 56 MET cc_start: 0.9138 (tpp) cc_final: 0.8568 (tpp) REVERT: D 76 ARG cc_start: 0.8612 (ttm110) cc_final: 0.8371 (ttm110) REVERT: G 64 GLU cc_start: 0.9262 (tm-30) cc_final: 0.8702 (tm-30) REVERT: G 73 ASN cc_start: 0.9582 (t0) cc_final: 0.9236 (t0) REVERT: G 92 GLU cc_start: 0.8264 (pm20) cc_final: 0.7953 (pm20) REVERT: G 104 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8574 (mm-40) REVERT: K 1 MET cc_start: 0.2581 (ptp) cc_final: 0.1942 (pmm) REVERT: K 52 PHE cc_start: 0.8639 (m-10) cc_final: 0.8282 (m-80) REVERT: K 78 ASN cc_start: 0.9470 (m-40) cc_final: 0.9207 (p0) REVERT: L 20 HIS cc_start: 0.7232 (m90) cc_final: 0.6577 (m90) REVERT: L 59 PHE cc_start: 0.8754 (m-80) cc_final: 0.7828 (m-10) REVERT: L 77 PHE cc_start: 0.8333 (t80) cc_final: 0.7746 (t80) outliers start: 4 outliers final: 3 residues processed: 101 average time/residue: 0.1218 time to fit residues: 17.2875 Evaluate side-chains 83 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain L residue 86 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 99 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 73 optimal weight: 30.0000 chunk 112 optimal weight: 8.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 75 HIS ** G 31 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 = 0.3515 r_free = 0.3515 target = 0.062285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.040438 restraints weight = 66520.004| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 2.92 r_work: 0.2586 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14357 Z= 0.180 Angle : 0.659 9.169 20619 Z= 0.372 Chirality : 0.045 0.252 2322 Planarity : 0.004 0.037 1605 Dihedral : 31.686 174.638 4250 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.51 % Allowed : 8.49 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.28), residues: 913 helix: 2.37 (0.22), residues: 556 sheet: -2.72 (0.68), residues: 36 loop : -1.07 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 74 TYR 0.030 0.002 TYR K 18 PHE 0.011 0.001 PHE C 25 TRP 0.024 0.003 TRP K 82 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.18 (14357) covalent geometry : angle 0.65880 / 0.37 (20619) hydrogen bonds : bond 0.05186 / 3.55 ( 771) hydrogen bonds : angle 3.45359 / 2.37 ( 1940) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8867 (tt0) cc_final: 0.8511 (tt0) REVERT: A 97 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8855 (mt-10) REVERT: C 90 ASP cc_start: 0.8796 (t0) cc_final: 0.8554 (t0) REVERT: D 76 ARG cc_start: 0.8703 (ttm110) cc_final: 0.8501 (ttm110) REVERT: F 63 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8681 (mp0) REVERT: G 73 ASN cc_start: 0.9603 (t0) cc_final: 0.9198 (t0) REVERT: H 105 LYS cc_start: 0.9220 (mtpt) cc_final: 0.8989 (mtmt) REVERT: K 1 MET cc_start: 0.2515 (ptp) cc_final: 0.1696 (pmm) REVERT: K 52 PHE cc_start: 0.8668 (m-10) cc_final: 0.8315 (m-80) REVERT: K 78 ASN cc_start: 0.9563 (m-40) cc_final: 0.9227 (p0) REVERT: L 20 HIS cc_start: 0.7221 (m90) cc_final: 0.6684 (m170) REVERT: L 40 LEU cc_start: 0.7196 (tp) cc_final: 0.6714 (tt) REVERT: L 59 PHE cc_start: 0.8739 (m-80) cc_final: 0.7747 (m-10) REVERT: L 77 PHE cc_start: 0.8662 (t80) cc_final: 0.7649 (t80) REVERT: L 82 TRP cc_start: 0.8157 (m100) cc_final: 0.7944 (m100) outliers start: 4 outliers final: 2 residues processed: 97 average time/residue: 0.1065 time to fit residues: 14.6297 Evaluate side-chains 89 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain L residue 86 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 71 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 108 optimal weight: 20.0000 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN K 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.061522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.039361 restraints weight = 65950.065| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 2.93 r_work: 0.2558 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9127 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14357 Z= 0.213 Angle : 0.660 8.867 20619 Z= 0.370 Chirality : 0.046 0.263 2322 Planarity : 0.004 0.037 1605 Dihedral : 31.522 164.747 4250 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.76 % Allowed : 11.28 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.28), residues: 913 helix: 2.28 (0.22), residues: 571 sheet: -2.42 (0.70), residues: 36 loop : -1.05 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 74 TYR 0.018 0.002 TYR K 18 PHE 0.015 0.002 PHE C 25 TRP 0.023 0.002 TRP K 82 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.21 (14357) covalent geometry : angle 0.65966 / 0.37 (20619) hydrogen bonds : bond 0.04864 / 3.32 ( 771) hydrogen bonds : angle 3.47440 / 2.39 ( 1940) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8874 (tt0) cc_final: 0.8509 (tt0) REVERT: A 97 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8784 (mt-10) REVERT: A 120 MET cc_start: 0.8814 (tpp) cc_final: 0.8578 (tpp) REVERT: D 56 MET cc_start: 0.9241 (tpp) cc_final: 0.8660 (tpp) REVERT: D 76 ARG cc_start: 0.8685 (ttm110) cc_final: 0.8454 (ttm110) REVERT: D 102 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8078 (tm-30) REVERT: G 64 GLU cc_start: 0.9308 (tm-30) cc_final: 0.8797 (tm-30) REVERT: G 73 ASN cc_start: 0.9609 (t0) cc_final: 0.9186 (t0) REVERT: H 105 LYS cc_start: 0.9212 (mtpt) cc_final: 0.8975 (mtmt) REVERT: K 52 PHE cc_start: 0.8657 (m-10) cc_final: 0.8317 (m-80) REVERT: K 78 ASN cc_start: 0.9559 (m-40) cc_final: 0.9242 (p0) REVERT: L 20 HIS cc_start: 0.7173 (m90) cc_final: 0.6676 (m170) REVERT: L 59 PHE cc_start: 0.8687 (m-80) cc_final: 0.7771 (m-10) REVERT: L 77 PHE cc_start: 0.8522 (t80) cc_final: 0.7378 (t80) outliers start: 6 outliers final: 3 residues processed: 96 average time/residue: 0.1312 time to fit residues: 17.1397 Evaluate side-chains 88 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain L residue 86 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 21 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 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 = 0.3474 r_free = 0.3474 target = 0.060566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.038407 restraints weight = 66597.945| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 2.96 r_work: 0.2529 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9148 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 14357 Z= 0.256 Angle : 0.694 8.903 20619 Z= 0.385 Chirality : 0.047 0.261 2322 Planarity : 0.004 0.039 1605 Dihedral : 31.458 167.224 4250 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.27 % Allowed : 12.93 % Favored : 85.80 % 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: 1.38 (0.28), residues: 913 helix: 2.10 (0.22), residues: 576 sheet: -2.05 (0.71), residues: 40 loop : -1.07 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 30 TYR 0.014 0.002 TYR A 54 PHE 0.024 0.002 PHE C 25 TRP 0.026 0.003 TRP K 82 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.26 (14357) covalent geometry : angle 0.69433 / 0.39 (20619) hydrogen bonds : bond 0.05297 / 3.59 ( 771) hydrogen bonds : angle 3.58781 / 2.46 ( 1940) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: D 56 MET cc_start: 0.9256 (tpp) cc_final: 0.8753 (tpp) REVERT: D 102 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8149 (tm-30) REVERT: E 39 HIS cc_start: 0.7754 (t-170) cc_final: 0.7353 (m170) REVERT: F 63 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8600 (mp0) REVERT: G 64 GLU cc_start: 0.9267 (tm-30) cc_final: 0.9043 (tm-30) REVERT: G 104 GLN cc_start: 0.9153 (mm-40) cc_final: 0.8903 (mm-40) REVERT: H 105 LYS cc_start: 0.9222 (mtpt) cc_final: 0.9005 (mtmt) REVERT: K 1 MET cc_start: 0.4167 (ptp) cc_final: 0.3441 (pmm) REVERT: K 52 PHE cc_start: 0.8669 (m-10) cc_final: 0.8316 (m-80) REVERT: K 78 ASN cc_start: 0.9584 (m-40) cc_final: 0.9298 (p0) REVERT: L 20 HIS cc_start: 0.7126 (m90) cc_final: 0.6788 (m170) REVERT: L 59 PHE cc_start: 0.8778 (m-80) cc_final: 0.7863 (m-10) REVERT: L 77 PHE cc_start: 0.8622 (t80) cc_final: 0.7785 (t80) outliers start: 10 outliers final: 6 residues processed: 97 average time/residue: 0.1339 time to fit residues: 17.9962 Evaluate side-chains 86 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain L residue 86 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 22 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 92 optimal weight: 0.1980 chunk 90 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 81 optimal weight: 20.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.061851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.039827 restraints weight = 65390.029| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.95 r_work: 0.2575 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9109 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14357 Z= 0.139 Angle : 0.610 9.027 20619 Z= 0.348 Chirality : 0.044 0.257 2322 Planarity : 0.004 0.054 1605 Dihedral : 31.292 169.039 4250 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.89 % Allowed : 13.31 % Favored : 85.80 % 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: 1.74 (0.28), residues: 913 helix: 2.44 (0.21), residues: 576 sheet: -2.14 (0.66), residues: 45 loop : -0.98 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 76 TYR 0.010 0.001 TYR B 88 PHE 0.012 0.001 PHE C 25 TRP 0.027 0.003 TRP K 82 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.14 (14357) covalent geometry : angle 0.60953 / 0.35 (20619) hydrogen bonds : bond 0.04315 / 2.97 ( 771) hydrogen bonds : angle 3.21001 / 2.21 ( 1940) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8817 (tt0) cc_final: 0.8597 (tt0) REVERT: D 56 MET cc_start: 0.9214 (tpp) cc_final: 0.8110 (tpp) REVERT: D 76 ARG cc_start: 0.8556 (ttm110) cc_final: 0.8325 (ttm110) REVERT: D 102 GLU cc_start: 0.8325 (tm-30) cc_final: 0.8104 (tm-30) REVERT: E 39 HIS cc_start: 0.7960 (t-170) cc_final: 0.7343 (m170) REVERT: G 64 GLU cc_start: 0.9261 (tm-30) cc_final: 0.8939 (tm-30) REVERT: G 73 ASN cc_start: 0.9589 (t0) cc_final: 0.9254 (t0) REVERT: G 104 GLN cc_start: 0.9145 (mm-40) cc_final: 0.8883 (mm-40) REVERT: H 105 LYS cc_start: 0.9180 (mtpt) cc_final: 0.8954 (mtmt) REVERT: K 1 MET cc_start: 0.3765 (ptp) cc_final: 0.3136 (pmm) REVERT: K 15 MET cc_start: 0.7271 (ptt) cc_final: 0.6209 (pmm) REVERT: K 52 PHE cc_start: 0.8640 (m-10) cc_final: 0.8282 (m-80) REVERT: K 78 ASN cc_start: 0.9571 (m-40) cc_final: 0.9256 (p0) REVERT: L 20 HIS cc_start: 0.7033 (m90) cc_final: 0.6679 (m170) REVERT: L 52 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7144 (t80) REVERT: L 59 PHE cc_start: 0.8753 (m-80) cc_final: 0.7841 (m-10) REVERT: L 77 PHE cc_start: 0.8332 (t80) cc_final: 0.7076 (t80) outliers start: 7 outliers final: 4 residues processed: 98 average time/residue: 0.1376 time to fit residues: 18.6449 Evaluate side-chains 90 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain L residue 52 PHE Chi-restraints excluded: chain L residue 86 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 109 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 113 optimal weight: 20.0000 chunk 110 optimal weight: 5.9990 chunk 108 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 38 ASN H 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.060124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.038006 restraints weight = 66905.243| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 2.97 r_work: 0.2511 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9169 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 14357 Z= 0.289 Angle : 0.721 8.418 20619 Z= 0.395 Chirality : 0.047 0.253 2322 Planarity : 0.005 0.041 1605 Dihedral : 31.392 172.032 4250 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.27 % Allowed : 14.20 % Favored : 84.54 % 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: 1.43 (0.28), residues: 913 helix: 2.14 (0.21), residues: 578 sheet: -2.13 (0.65), residues: 47 loop : -1.03 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 76 TYR 0.012 0.002 TYR A 54 PHE 0.027 0.002 PHE C 25 TRP 0.029 0.003 TRP K 82 HIS 0.006 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.29 (14357) covalent geometry : angle 0.72051 / 0.39 (20619) hydrogen bonds : bond 0.05498 / 3.72 ( 771) hydrogen bonds : angle 3.61462 / 2.49 ( 1940) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: D 56 MET cc_start: 0.9229 (tpp) cc_final: 0.8791 (tpp) REVERT: D 102 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7975 (tm-30) REVERT: E 115 LYS cc_start: 0.9558 (mmmm) cc_final: 0.9294 (mmtt) REVERT: G 64 GLU cc_start: 0.9313 (tm-30) cc_final: 0.9089 (tm-30) REVERT: G 73 ASN cc_start: 0.9602 (t0) cc_final: 0.9195 (t0) REVERT: G 75 LYS cc_start: 0.9609 (mmmm) cc_final: 0.9181 (mmmm) REVERT: H 105 LYS cc_start: 0.9192 (mtpt) cc_final: 0.8984 (mtmt) REVERT: K 52 PHE cc_start: 0.8653 (m-10) cc_final: 0.8322 (m-80) REVERT: K 78 ASN cc_start: 0.9583 (m-40) cc_final: 0.9272 (p0) REVERT: L 20 HIS cc_start: 0.7028 (m90) cc_final: 0.6592 (m170) REVERT: L 52 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.7002 (t80) REVERT: L 59 PHE cc_start: 0.8720 (m-80) cc_final: 0.7886 (m-10) REVERT: L 77 PHE cc_start: 0.8318 (t80) cc_final: 0.7132 (t80) outliers start: 10 outliers final: 9 residues processed: 90 average time/residue: 0.1273 time to fit residues: 15.8960 Evaluate side-chains 91 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain L residue 52 PHE Chi-restraints excluded: chain L residue 86 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 72 optimal weight: 0.7980 chunk 95 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 82 optimal weight: 20.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.060999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.038973 restraints weight = 65766.131| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 2.92 r_work: 0.2545 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9135 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14357 Z= 0.176 Angle : 0.635 8.862 20619 Z= 0.357 Chirality : 0.044 0.231 2322 Planarity : 0.004 0.054 1605 Dihedral : 31.304 176.184 4250 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.89 % Allowed : 14.96 % Favored : 84.16 % 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: 1.68 (0.28), residues: 913 helix: 2.39 (0.22), residues: 577 sheet: -2.39 (0.64), residues: 49 loop : -0.96 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 76 TYR 0.008 0.001 TYR F 51 PHE 0.016 0.001 PHE C 25 TRP 0.029 0.002 TRP K 82 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.18 (14357) covalent geometry : angle 0.63480 / 0.36 (20619) hydrogen bonds : bond 0.04536 / 3.10 ( 771) hydrogen bonds : angle 3.32571 / 2.29 ( 1940) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: D 56 MET cc_start: 0.9240 (tpp) cc_final: 0.8974 (tpp) REVERT: D 102 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7998 (tm-30) REVERT: E 105 GLU cc_start: 0.8016 (pp20) cc_final: 0.7513 (pp20) REVERT: E 115 LYS cc_start: 0.9566 (mmmm) cc_final: 0.9287 (mmtt) REVERT: G 64 GLU cc_start: 0.9296 (tm-30) cc_final: 0.8974 (tm-30) REVERT: G 73 ASN cc_start: 0.9623 (t0) cc_final: 0.9173 (t0) REVERT: G 75 LYS cc_start: 0.9572 (mmmm) cc_final: 0.9249 (mmmm) REVERT: G 104 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8790 (mm-40) REVERT: H 105 LYS cc_start: 0.9198 (mtpt) cc_final: 0.8961 (mtmt) REVERT: K 1 MET cc_start: 0.3660 (ptp) cc_final: 0.3365 (pmm) REVERT: K 15 MET cc_start: 0.7450 (ptt) cc_final: 0.6296 (pmm) REVERT: K 52 PHE cc_start: 0.8646 (m-10) cc_final: 0.8307 (m-80) REVERT: K 78 ASN cc_start: 0.9587 (m-40) cc_final: 0.9289 (p0) REVERT: L 20 HIS cc_start: 0.7062 (m90) cc_final: 0.6754 (m170) REVERT: L 52 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.7322 (t80) REVERT: L 59 PHE cc_start: 0.8697 (m-80) cc_final: 0.7886 (m-10) REVERT: L 77 PHE cc_start: 0.8261 (t80) cc_final: 0.7036 (t80) outliers start: 7 outliers final: 5 residues processed: 93 average time/residue: 0.1272 time to fit residues: 16.4376 Evaluate side-chains 92 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain L residue 52 PHE Chi-restraints excluded: chain L residue 86 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 92 optimal weight: 30.0000 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 116 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 82 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 chunk 41 optimal weight: 0.4980 chunk 97 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.059443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.037362 restraints weight = 66450.450| |-----------------------------------------------------------------------------| r_work (start): 0.2668 rms_B_bonded: 2.98 r_work: 0.2490 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9169 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 14357 Z= 0.337 Angle : 0.762 9.326 20619 Z= 0.414 Chirality : 0.048 0.246 2322 Planarity : 0.005 0.064 1605 Dihedral : 31.440 179.710 4250 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.52 % Allowed : 14.58 % Favored : 83.90 % 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: 1.12 (0.28), residues: 913 helix: 1.91 (0.21), residues: 577 sheet: -2.58 (0.63), residues: 49 loop : -1.06 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 76 TYR 0.014 0.002 TYR D 39 PHE 0.028 0.002 PHE C 25 TRP 0.029 0.003 TRP K 82 HIS 0.007 0.002 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00703 / 0.34 (14357) covalent geometry : angle 0.76222 / 0.41 (20619) hydrogen bonds : bond 0.06028 / 4.07 ( 771) hydrogen bonds : angle 3.75935 / 2.60 ( 1940) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: D 56 MET cc_start: 0.9260 (tpp) cc_final: 0.8474 (tpp) REVERT: D 102 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8111 (tm-30) REVERT: E 59 GLU cc_start: 0.8818 (pp20) cc_final: 0.8458 (pp20) REVERT: E 115 LYS cc_start: 0.9597 (mmmm) cc_final: 0.9285 (mmtt) REVERT: G 64 GLU cc_start: 0.9304 (tm-30) cc_final: 0.9058 (tm-30) REVERT: K 1 MET cc_start: 0.3889 (ptp) cc_final: 0.3538 (pmm) REVERT: K 15 MET cc_start: 0.7660 (ptt) cc_final: 0.7431 (ptt) REVERT: K 52 PHE cc_start: 0.8719 (m-10) cc_final: 0.8330 (m-80) REVERT: K 78 ASN cc_start: 0.9619 (m-40) cc_final: 0.9337 (p0) REVERT: L 20 HIS cc_start: 0.6899 (m90) cc_final: 0.6554 (m170) REVERT: L 52 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.6875 (t80) REVERT: L 59 PHE cc_start: 0.8691 (m-80) cc_final: 0.8082 (m-10) REVERT: L 77 PHE cc_start: 0.8225 (t80) cc_final: 0.6975 (t80) outliers start: 12 outliers final: 10 residues processed: 93 average time/residue: 0.1296 time to fit residues: 16.8815 Evaluate side-chains 92 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain L residue 52 PHE Chi-restraints excluded: chain L residue 86 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 104 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 96 optimal weight: 10.9990 chunk 115 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 60 optimal weight: 0.0010 chunk 92 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.060323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.038214 restraints weight = 65144.762| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 2.89 r_work: 0.2523 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9143 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14357 Z= 0.205 Angle : 0.669 10.472 20619 Z= 0.373 Chirality : 0.045 0.246 2322 Planarity : 0.004 0.062 1605 Dihedral : 31.324 177.190 4250 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.14 % Allowed : 14.96 % Favored : 83.90 % 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: 1.48 (0.28), residues: 913 helix: 2.23 (0.22), residues: 577 sheet: -2.55 (0.64), residues: 49 loop : -1.00 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 76 TYR 0.009 0.001 TYR F 51 PHE 0.019 0.002 PHE C 25 TRP 0.029 0.002 TRP K 82 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.20 (14357) covalent geometry : angle 0.66923 / 0.37 (20619) hydrogen bonds : bond 0.04791 / 3.26 ( 771) hydrogen bonds : angle 3.44933 / 2.38 ( 1940) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: D 56 MET cc_start: 0.9247 (tpp) cc_final: 0.8980 (tpp) REVERT: D 102 GLU cc_start: 0.8272 (tm-30) cc_final: 0.8002 (tm-30) REVERT: E 59 GLU cc_start: 0.8842 (pp20) cc_final: 0.8460 (pp20) REVERT: E 105 GLU cc_start: 0.7869 (pp20) cc_final: 0.7418 (pp20) REVERT: E 115 LYS cc_start: 0.9582 (mmmm) cc_final: 0.9249 (mmtt) REVERT: G 64 GLU cc_start: 0.9286 (tm-30) cc_final: 0.9011 (tm-30) REVERT: H 105 LYS cc_start: 0.9220 (mtpt) cc_final: 0.8986 (mtmt) REVERT: K 1 MET cc_start: 0.3757 (ptp) cc_final: 0.3454 (pmm) REVERT: K 15 MET cc_start: 0.7700 (ptt) cc_final: 0.7480 (ptt) REVERT: K 52 PHE cc_start: 0.8648 (m-10) cc_final: 0.8158 (m-80) REVERT: K 78 ASN cc_start: 0.9612 (m-40) cc_final: 0.9325 (p0) REVERT: L 20 HIS cc_start: 0.6869 (m90) cc_final: 0.6147 (m170) REVERT: L 52 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.6910 (t80) REVERT: L 59 PHE cc_start: 0.8778 (m-80) cc_final: 0.8065 (m-10) REVERT: L 77 PHE cc_start: 0.8153 (t80) cc_final: 0.6866 (t80) outliers start: 9 outliers final: 6 residues processed: 95 average time/residue: 0.1201 time to fit residues: 15.9360 Evaluate side-chains 93 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain L residue 52 PHE Chi-restraints excluded: chain L residue 86 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 71 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 83 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 55 optimal weight: 0.0170 chunk 104 optimal weight: 10.0000 overall best weight: 1.5622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.060823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.038676 restraints weight = 65339.197| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 2.92 r_work: 0.2534 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9135 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14357 Z= 0.175 Angle : 0.655 10.277 20619 Z= 0.367 Chirality : 0.044 0.258 2322 Planarity : 0.004 0.059 1605 Dihedral : 31.221 176.294 4250 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.01 % Allowed : 15.72 % Favored : 83.27 % 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: 1.67 (0.28), residues: 913 helix: 2.37 (0.22), residues: 577 sheet: -2.33 (0.66), residues: 45 loop : -0.98 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 76 TYR 0.010 0.001 TYR F 51 PHE 0.016 0.002 PHE C 25 TRP 0.029 0.002 TRP K 82 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 (14357) covalent geometry : angle 0.65526 / 0.37 (20619) hydrogen bonds : bond 0.04537 / 3.10 ( 771) hydrogen bonds : angle 3.37181 / 2.32 ( 1940) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3041.79 seconds wall clock time: 52 minutes 35.30 seconds (3155.30 seconds total)