Starting phenix.real_space_refine on Thu Aug 6 03:22:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pep_17634/08_2026/8pep_17634.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pep_17634/08_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_17634/08_2026/8pep_17634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pep_17634/08_2026/8pep_17634.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8pep_17634/08_2026/8pep_17634.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pep_17634/08_2026/8pep_17634.cif" model { file = "/net/cci-nas-00/data/ceres_data/8pep_17634/08_2026/8pep_17634.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pep_17634/08_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-2.2rc3-6140/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: 3.04, per 1000 atoms: 0.23 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: 0.88 Conformation dependent library (CDL) restraints added in 483.8 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: 1.78 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: 1.87 Time building geometry restraints manager: 1.36 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: 20321 2.72 - 5.44: 282 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: 0.600 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 13.000 Find NCS groups from input model: 0.150 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:1.170 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.410 ------------------------------------------------------------------------------- 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= 0.483 Angle : 0.863 13.598 20619 Z= 0.727 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 0.86295 / 0.73 (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 : 0.381 Fit side-chains revert: symmetry clash REVERT: E 56 LYS cc_start: 0.8835 (mtpp) cc_final: 0.8595 (mtmm) REVERT: G 38 ASN cc_start: 0.7909 (m-40) cc_final: 0.7457 (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: 0.8986 (m-40) REVERT: L 20 HIS cc_start: 0.7653 (m-70) cc_final: 0.7021 (m170) REVERT: L 59 PHE cc_start: 0.8454 (m-80) cc_final: 0.7893 (m-80) REVERT: L 77 PHE cc_start: 0.8300 (t80) cc_final: 0.7716 (t80) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.1568 time to fit residues: 32.3866 Evaluate side-chains 86 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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: 4.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 20.0000 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 = 0.3534 r_free = 0.3534 target = 0.063249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.041473 restraints weight = 64963.622| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.87 r_work: 0.2620 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14357 Z= 0.158 Angle : 0.714 9.302 20619 Z= 0.398 Chirality : 0.049 0.348 2322 Planarity : 0.005 0.044 1605 Dihedral : 32.026 178.901 4250 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.75 % Favored : 98.14 % Rotamer: Outliers : 0.63 % Allowed : 7.86 % 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: 1.22 (0.28), residues: 913 helix: 2.04 (0.22), residues: 563 sheet: -2.49 (1.01), residues: 22 loop : -1.19 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 35 TYR 0.028 0.002 TYR L 61 PHE 0.019 0.002 PHE L 5 TRP 0.017 0.004 TRP K 82 HIS 0.009 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.16 (14357) covalent geometry : angle 0.71361 / 0.40 (20619) hydrogen bonds : bond 0.05538 / 3.84 ( 771) hydrogen bonds : angle 3.57455 / 2.46 ( 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 105 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: D 32 GLU cc_start: 0.8870 (pm20) cc_final: 0.8638 (pm20) REVERT: D 56 MET cc_start: 0.9100 (tpp) cc_final: 0.8550 (tpp) REVERT: D 76 ARG cc_start: 0.8613 (ttm110) cc_final: 0.8369 (ttm110) REVERT: G 64 GLU cc_start: 0.9277 (tm-30) cc_final: 0.8717 (tm-30) REVERT: G 73 ASN cc_start: 0.9589 (t0) cc_final: 0.9253 (t0) REVERT: G 92 GLU cc_start: 0.8299 (pm20) cc_final: 0.7527 (pm20) REVERT: G 104 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8583 (mm-40) REVERT: K 1 MET cc_start: 0.2555 (ptp) cc_final: 0.1927 (pmm) REVERT: K 52 PHE cc_start: 0.8644 (m-10) cc_final: 0.8284 (m-80) REVERT: K 78 ASN cc_start: 0.9471 (m-40) cc_final: 0.9202 (p0) REVERT: L 20 HIS cc_start: 0.7200 (m90) cc_final: 0.6593 (m90) REVERT: L 59 PHE cc_start: 0.8755 (m-80) cc_final: 0.7812 (m-10) REVERT: L 77 PHE cc_start: 0.8333 (t80) cc_final: 0.7817 (t80) outliers start: 5 outliers final: 3 residues processed: 104 average time/residue: 0.1240 time to fit residues: 18.0214 Evaluate side-chains 84 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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: 2.9990 chunk 19 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 73 optimal weight: 30.0000 chunk 112 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 ASN D 106 HIS F 75 HIS G 31 HIS G 38 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.062452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.040431 restraints weight = 66703.470| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 2.97 r_work: 0.2586 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9096 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14357 Z= 0.178 Angle : 0.668 8.986 20619 Z= 0.375 Chirality : 0.046 0.286 2322 Planarity : 0.004 0.037 1605 Dihedral : 31.621 175.140 4250 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.51 % Allowed : 9.13 % Favored : 90.37 % 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: 1.42 (0.28), residues: 913 helix: 2.29 (0.22), residues: 562 sheet: -2.73 (0.68), residues: 36 loop : -1.16 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 99 TYR 0.027 0.002 TYR K 18 PHE 0.011 0.001 PHE C 25 TRP 0.022 0.003 TRP K 82 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.18 (14357) covalent geometry : angle 0.66764 / 0.37 (20619) hydrogen bonds : bond 0.05212 / 3.58 ( 771) hydrogen bonds : angle 3.46263 / 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 : 0.369 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8872 (tt0) cc_final: 0.8522 (tt0) REVERT: C 36 LYS cc_start: 0.9021 (mtmt) cc_final: 0.8812 (mtmt) REVERT: C 72 ASP cc_start: 0.9235 (t0) cc_final: 0.8560 (m-30) REVERT: C 92 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7794 (mt-10) REVERT: D 56 MET cc_start: 0.9120 (tpp) cc_final: 0.8637 (tpp) REVERT: D 76 ARG cc_start: 0.8692 (ttm110) cc_final: 0.8486 (ttm110) REVERT: F 63 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8592 (mp0) REVERT: G 73 ASN cc_start: 0.9594 (t0) cc_final: 0.9188 (t0) REVERT: H 105 LYS cc_start: 0.9222 (mtpt) cc_final: 0.8995 (mtmt) REVERT: K 1 MET cc_start: 0.2557 (ptp) cc_final: 0.1739 (pmm) REVERT: K 52 PHE cc_start: 0.8673 (m-10) cc_final: 0.8316 (m-80) REVERT: K 78 ASN cc_start: 0.9562 (m-40) cc_final: 0.9222 (p0) REVERT: L 20 HIS cc_start: 0.7253 (m90) cc_final: 0.6675 (m170) REVERT: L 40 LEU cc_start: 0.7272 (tp) cc_final: 0.6797 (tt) REVERT: L 59 PHE cc_start: 0.8733 (m-80) cc_final: 0.7767 (m-10) REVERT: L 77 PHE cc_start: 0.8735 (t80) cc_final: 0.7754 (t80) outliers start: 4 outliers final: 2 residues processed: 98 average time/residue: 0.1256 time to fit residues: 17.1321 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 : 0.300 ------------------------------------------------------------------------------- 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: 4.9990 chunk 97 optimal weight: 10.9990 chunk 106 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 ASN G 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.061332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.039184 restraints weight = 65944.495| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.94 r_work: 0.2552 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9133 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 14357 Z= 0.232 Angle : 0.693 8.716 20619 Z= 0.382 Chirality : 0.047 0.291 2322 Planarity : 0.004 0.037 1605 Dihedral : 31.470 167.190 4250 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.89 % Allowed : 10.90 % Favored : 88.21 % 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: 1.47 (0.28), residues: 913 helix: 2.23 (0.22), residues: 571 sheet: -2.45 (0.69), residues: 36 loop : -1.08 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 42 TYR 0.013 0.002 TYR G 50 PHE 0.015 0.002 PHE C 25 TRP 0.022 0.003 TRP K 82 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.23 (14357) covalent geometry : angle 0.69258 / 0.38 (20619) hydrogen bonds : bond 0.05032 / 3.44 ( 771) hydrogen bonds : angle 3.54066 / 2.43 ( 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 98 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8827 (tpp) cc_final: 0.8623 (tpp) REVERT: D 56 MET cc_start: 0.9239 (tpp) cc_final: 0.8770 (tpp) REVERT: G 64 GLU cc_start: 0.9300 (tm-30) cc_final: 0.8775 (tm-30) REVERT: G 73 ASN cc_start: 0.9611 (t0) cc_final: 0.9190 (t0) REVERT: H 105 LYS cc_start: 0.9219 (mtpt) cc_final: 0.8980 (mtmt) REVERT: K 15 MET cc_start: 0.7961 (ppp) cc_final: 0.7744 (ptt) REVERT: K 52 PHE cc_start: 0.8662 (m-10) cc_final: 0.8321 (m-80) REVERT: K 78 ASN cc_start: 0.9563 (m-40) cc_final: 0.9220 (p0) REVERT: L 20 HIS cc_start: 0.7200 (m90) cc_final: 0.6719 (m170) REVERT: L 59 PHE cc_start: 0.8691 (m-80) cc_final: 0.7781 (m-10) REVERT: L 77 PHE cc_start: 0.8645 (t80) cc_final: 0.7631 (t80) outliers start: 7 outliers final: 4 residues processed: 96 average time/residue: 0.1556 time to fit residues: 20.4800 Evaluate side-chains 85 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS 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: 2.9990 chunk 79 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 113 optimal weight: 30.0000 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.061309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.039267 restraints weight = 66055.197| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.95 r_work: 0.2552 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9125 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14357 Z= 0.198 Angle : 0.655 8.927 20619 Z= 0.367 Chirality : 0.046 0.284 2322 Planarity : 0.004 0.049 1605 Dihedral : 31.305 165.203 4250 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.14 % Allowed : 12.67 % Favored : 86.19 % 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: 1.58 (0.28), residues: 913 helix: 2.30 (0.22), residues: 576 sheet: -2.12 (0.72), residues: 40 loop : -1.05 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 76 TYR 0.012 0.002 TYR G 50 PHE 0.018 0.002 PHE C 25 TRP 0.026 0.003 TRP K 82 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.20 (14357) covalent geometry : angle 0.65517 / 0.37 (20619) hydrogen bonds : bond 0.04682 / 3.20 ( 771) hydrogen bonds : angle 3.41062 / 2.34 ( 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 101 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8831 (tt0) cc_final: 0.8576 (tt0) REVERT: C 90 ASP cc_start: 0.8624 (t0) cc_final: 0.8220 (t0) REVERT: D 56 MET cc_start: 0.9237 (tpp) cc_final: 0.9017 (tpp) REVERT: G 64 GLU cc_start: 0.9252 (tm-30) cc_final: 0.9008 (tm-30) REVERT: G 73 ASN cc_start: 0.9620 (t0) cc_final: 0.9120 (t0) REVERT: G 75 LYS cc_start: 0.9522 (mmmm) cc_final: 0.9207 (mmmm) REVERT: H 105 LYS cc_start: 0.9208 (mtpt) cc_final: 0.8974 (mtmt) REVERT: K 1 MET cc_start: 0.4074 (ptp) cc_final: 0.3362 (pmm) REVERT: K 15 MET cc_start: 0.8195 (ppp) cc_final: 0.7908 (ptt) REVERT: K 52 PHE cc_start: 0.8657 (m-10) cc_final: 0.8319 (m-80) REVERT: K 78 ASN cc_start: 0.9563 (m-40) cc_final: 0.9226 (p0) REVERT: L 20 HIS cc_start: 0.7131 (m90) cc_final: 0.6712 (m170) REVERT: L 59 PHE cc_start: 0.8723 (m-80) cc_final: 0.7788 (m-10) REVERT: L 77 PHE cc_start: 0.8619 (t80) cc_final: 0.7527 (t80) outliers start: 9 outliers final: 5 residues processed: 99 average time/residue: 0.1526 time to fit residues: 20.7270 Evaluate side-chains 89 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 63 GLU 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: 0.7980 chunk 72 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 92 optimal weight: 0.0030 chunk 90 optimal weight: 2.9990 chunk 112 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 81 optimal weight: 20.0000 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 ASN E 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.062149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.040276 restraints weight = 65577.322| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.96 r_work: 0.2589 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9095 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14357 Z= 0.132 Angle : 0.613 9.001 20619 Z= 0.348 Chirality : 0.044 0.292 2322 Planarity : 0.004 0.052 1605 Dihedral : 31.158 165.724 4250 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.51 % Allowed : 13.81 % Favored : 85.68 % 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 (0.28), residues: 913 helix: 2.50 (0.22), residues: 576 sheet: -2.15 (0.67), residues: 45 loop : -0.92 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 76 TYR 0.010 0.001 TYR B 88 PHE 0.009 0.001 PHE F 61 TRP 0.026 0.003 TRP K 82 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.13 (14357) covalent geometry : angle 0.61332 / 0.35 (20619) hydrogen bonds : bond 0.04215 / 2.91 ( 771) hydrogen bonds : angle 3.17786 / 2.19 ( 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 94 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8791 (tt0) cc_final: 0.8504 (tt0) REVERT: D 56 MET cc_start: 0.9225 (tpp) cc_final: 0.8123 (tpp) REVERT: D 76 ARG cc_start: 0.8563 (ttm110) cc_final: 0.8323 (ttm110) REVERT: E 39 HIS cc_start: 0.7741 (t-170) cc_final: 0.7194 (m170) REVERT: G 64 GLU cc_start: 0.9285 (tm-30) cc_final: 0.8782 (tm-30) REVERT: G 73 ASN cc_start: 0.9610 (t0) cc_final: 0.9112 (t0) REVERT: G 75 LYS cc_start: 0.9456 (mmmm) cc_final: 0.9128 (mmmm) REVERT: H 105 LYS cc_start: 0.9188 (mtpt) cc_final: 0.8969 (mtmt) REVERT: K 1 MET cc_start: 0.3720 (ptp) cc_final: 0.3106 (pmm) REVERT: K 15 MET cc_start: 0.8148 (ppp) cc_final: 0.7728 (ptt) REVERT: K 52 PHE cc_start: 0.8634 (m-10) cc_final: 0.8283 (m-80) REVERT: K 78 ASN cc_start: 0.9492 (m-40) cc_final: 0.9225 (p0) REVERT: L 77 PHE cc_start: 0.8368 (t80) cc_final: 0.7476 (t80) outliers start: 4 outliers final: 3 residues processed: 93 average time/residue: 0.1496 time to fit residues: 19.0986 Evaluate side-chains 86 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 109 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 113 optimal weight: 20.0000 chunk 110 optimal weight: 6.9990 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: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.060623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.038528 restraints weight = 66729.039| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 2.95 r_work: 0.2534 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9144 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 14357 Z= 0.254 Angle : 0.699 9.053 20619 Z= 0.383 Chirality : 0.046 0.277 2322 Planarity : 0.004 0.039 1605 Dihedral : 31.260 167.448 4250 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.39 % Allowed : 14.20 % Favored : 84.41 % 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 (0.28), residues: 913 helix: 2.27 (0.22), residues: 583 sheet: -2.10 (0.67), residues: 45 loop : -1.01 (0.34), residues: 285 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 0.020 0.002 PHE C 25 TRP 0.027 0.004 TRP K 82 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.25 (14357) covalent geometry : angle 0.69909 / 0.38 (20619) hydrogen bonds : bond 0.05087 / 3.46 ( 771) hydrogen bonds : angle 3.52336 / 2.43 ( 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 97 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8856 (tpp) cc_final: 0.8641 (tpp) REVERT: D 56 MET cc_start: 0.9233 (tpp) cc_final: 0.8779 (tpp) REVERT: G 64 GLU cc_start: 0.9330 (tm-30) cc_final: 0.9083 (tm-30) REVERT: H 105 LYS cc_start: 0.9222 (mtpt) cc_final: 0.8986 (mtmt) REVERT: K 15 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7926 (ptp) REVERT: K 52 PHE cc_start: 0.8636 (m-10) cc_final: 0.8318 (m-80) REVERT: K 78 ASN cc_start: 0.9553 (m-40) cc_final: 0.9219 (p0) REVERT: L 20 HIS cc_start: 0.5840 (m-70) cc_final: 0.5243 (m-70) REVERT: L 52 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7706 (t80) REVERT: L 77 PHE cc_start: 0.8405 (t80) cc_final: 0.7354 (t80) outliers start: 11 outliers final: 8 residues processed: 92 average time/residue: 0.1479 time to fit residues: 18.9875 Evaluate side-chains 89 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS 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 K residue 15 MET 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: 4.9990 chunk 4 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 32 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 82 optimal weight: 20.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 ASN E 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.061319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.039287 restraints weight = 65819.556| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 2.95 r_work: 0.2556 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9129 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14357 Z= 0.173 Angle : 0.648 9.653 20619 Z= 0.361 Chirality : 0.045 0.269 2322 Planarity : 0.004 0.060 1605 Dihedral : 31.191 170.365 4250 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.63 % Allowed : 15.46 % 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: 1.84 (0.28), residues: 913 helix: 2.41 (0.22), residues: 582 sheet: -1.94 (0.73), residues: 40 loop : -0.82 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 76 TYR 0.008 0.001 TYR F 51 PHE 0.060 0.002 PHE L 59 TRP 0.029 0.003 TRP K 82 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.17 (14357) covalent geometry : angle 0.64835 / 0.36 (20619) hydrogen bonds : bond 0.04436 / 3.03 ( 771) hydrogen bonds : angle 3.30510 / 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 91 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: D 56 MET cc_start: 0.9257 (tpp) cc_final: 0.8127 (tpp) REVERT: E 39 HIS cc_start: 0.7787 (t-170) cc_final: 0.7161 (m170) REVERT: E 105 GLU cc_start: 0.8095 (pp20) cc_final: 0.7516 (pp20) REVERT: G 64 GLU cc_start: 0.9317 (tm-30) cc_final: 0.8994 (tm-30) REVERT: G 73 ASN cc_start: 0.9569 (t0) cc_final: 0.9276 (t0) REVERT: H 105 LYS cc_start: 0.9214 (mtpt) cc_final: 0.8989 (mtmt) REVERT: K 1 MET cc_start: 0.3655 (ptp) cc_final: 0.3096 (pmm) REVERT: K 15 MET cc_start: 0.8053 (ppp) cc_final: 0.7683 (ptt) REVERT: K 52 PHE cc_start: 0.8640 (m-10) cc_final: 0.8311 (m-80) REVERT: K 78 ASN cc_start: 0.9496 (m-40) cc_final: 0.9235 (p0) REVERT: L 20 HIS cc_start: 0.5930 (m-70) cc_final: 0.5543 (m-70) REVERT: L 52 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7763 (t80) REVERT: L 59 PHE cc_start: 0.8646 (t80) cc_final: 0.8249 (t80) outliers start: 5 outliers final: 4 residues processed: 89 average time/residue: 0.1568 time to fit residues: 19.1416 Evaluate side-chains 89 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 92 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 82 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 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 = 0.3467 r_free = 0.3467 target = 0.060169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.038042 restraints weight = 66020.501| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 2.93 r_work: 0.2515 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9151 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 14357 Z= 0.271 Angle : 0.729 9.451 20619 Z= 0.396 Chirality : 0.047 0.259 2322 Planarity : 0.005 0.063 1605 Dihedral : 31.287 175.582 4250 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.89 % Allowed : 15.34 % Favored : 83.78 % 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: 1.45 (0.28), residues: 913 helix: 2.15 (0.21), residues: 577 sheet: -2.30 (0.66), residues: 45 loop : -0.94 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 76 TYR 0.011 0.002 TYR A 54 PHE 0.042 0.002 PHE L 59 TRP 0.032 0.004 TRP L 82 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.27 (14357) covalent geometry : angle 0.72912 / 0.40 (20619) hydrogen bonds : bond 0.05451 / 3.69 ( 771) hydrogen bonds : angle 3.59851 / 2.48 ( 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 90 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: D 56 MET cc_start: 0.9274 (tpp) cc_final: 0.8818 (tpp) REVERT: E 59 GLU cc_start: 0.8567 (pp20) cc_final: 0.8229 (pp20) REVERT: G 64 GLU cc_start: 0.9313 (tm-30) cc_final: 0.9052 (tm-30) REVERT: G 73 ASN cc_start: 0.9592 (t0) cc_final: 0.9224 (t0) REVERT: G 75 LYS cc_start: 0.9588 (mmmm) cc_final: 0.9300 (mmmm) REVERT: H 105 LYS cc_start: 0.9241 (mtpt) cc_final: 0.9032 (mtmt) REVERT: K 1 MET cc_start: 0.3788 (ptp) cc_final: 0.3472 (pmm) REVERT: K 52 PHE cc_start: 0.8635 (m-10) cc_final: 0.8325 (m-80) REVERT: K 78 ASN cc_start: 0.9584 (m-40) cc_final: 0.9276 (p0) REVERT: L 20 HIS cc_start: 0.5858 (m-70) cc_final: 0.5515 (m-70) REVERT: L 52 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7536 (t80) REVERT: L 59 PHE cc_start: 0.8598 (t80) cc_final: 0.8045 (t80) outliers start: 7 outliers final: 5 residues processed: 86 average time/residue: 0.1571 time to fit residues: 18.6358 Evaluate side-chains 85 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR 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 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: 10.0000 chunk 78 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 115 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 60 optimal weight: 0.4980 chunk 92 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.061475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.039325 restraints weight = 64999.709| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 2.92 r_work: 0.2558 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14357 Z= 0.146 Angle : 0.642 10.210 20619 Z= 0.360 Chirality : 0.044 0.272 2322 Planarity : 0.004 0.063 1605 Dihedral : 31.135 178.373 4250 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.63 % Allowed : 15.59 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.28), residues: 913 helix: 2.48 (0.22), residues: 577 sheet: -2.23 (0.67), residues: 45 loop : -0.81 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 76 TYR 0.008 0.001 TYR F 51 PHE 0.040 0.002 PHE L 59 TRP 0.031 0.004 TRP K 82 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.15 (14357) covalent geometry : angle 0.64245 / 0.36 (20619) hydrogen bonds : bond 0.04360 / 2.99 ( 771) hydrogen bonds : angle 3.24599 / 2.24 ( 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 95 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8661 (tt0) cc_final: 0.8448 (tt0) REVERT: D 56 MET cc_start: 0.9275 (tpp) cc_final: 0.8158 (tpp) REVERT: D 76 ARG cc_start: 0.8680 (ttm110) cc_final: 0.8476 (ttm110) REVERT: E 39 HIS cc_start: 0.7812 (t-170) cc_final: 0.7163 (m170) REVERT: E 105 GLU cc_start: 0.7946 (pp20) cc_final: 0.7512 (pp20) REVERT: G 64 GLU cc_start: 0.9291 (tm-30) cc_final: 0.8946 (tm-30) REVERT: G 73 ASN cc_start: 0.9597 (t0) cc_final: 0.9222 (t0) REVERT: G 75 LYS cc_start: 0.9523 (mmmm) cc_final: 0.9266 (mmmm) REVERT: H 68 GLU cc_start: 0.9092 (tp30) cc_final: 0.8876 (tp30) REVERT: H 105 LYS cc_start: 0.9218 (mtpt) cc_final: 0.8991 (mtmt) REVERT: K 1 MET cc_start: 0.3683 (ptp) cc_final: 0.3170 (pmm) REVERT: K 52 PHE cc_start: 0.8687 (m-10) cc_final: 0.8331 (m-80) REVERT: K 78 ASN cc_start: 0.9510 (m-40) cc_final: 0.9269 (p0) REVERT: L 20 HIS cc_start: 0.5853 (m-70) cc_final: 0.5477 (m-70) REVERT: L 52 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7601 (t80) REVERT: L 59 PHE cc_start: 0.8628 (t80) cc_final: 0.8147 (t80) outliers start: 5 outliers final: 3 residues processed: 93 average time/residue: 0.1443 time to fit residues: 18.5626 Evaluate side-chains 90 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 71 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 55 optimal weight: 0.0060 chunk 104 optimal weight: 9.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 ASN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.061729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.039659 restraints weight = 65218.431| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.96 r_work: 0.2567 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9111 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14357 Z= 0.136 Angle : 0.633 10.093 20619 Z= 0.354 Chirality : 0.043 0.281 2322 Planarity : 0.004 0.065 1605 Dihedral : 31.068 178.925 4250 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.51 % Allowed : 15.21 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.28), residues: 913 helix: 2.56 (0.22), residues: 577 sheet: -2.11 (0.72), residues: 41 loop : -0.67 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 76 TYR 0.009 0.001 TYR H 37 PHE 0.039 0.002 PHE L 59 TRP 0.033 0.004 TRP K 82 HIS 0.007 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.14 (14357) covalent geometry : angle 0.63344 / 0.35 (20619) hydrogen bonds : bond 0.04279 / 2.94 ( 771) hydrogen bonds : angle 3.18204 / 2.19 ( 1940) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3233.11 seconds wall clock time: 55 minutes 59.27 seconds (3359.27 seconds total)