Starting phenix.real_space_refine on Wed Aug 5 20:42:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8euj_28614/08_2026/8euj_28614_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8euj_28614/08_2026/8euj_28614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8euj_28614/08_2026/8euj_28614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8euj_28614/08_2026/8euj_28614.map" model { file = "/net/cci-nas-00/data/ceres_data/8euj_28614/08_2026/8euj_28614_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8euj_28614/08_2026/8euj_28614_neut.cif" } resolution = 3.36 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= 0.004 sd= 0.104 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 292 5.49 5 S 12 5.16 5 C 6591 2.51 5 N 2205 2.21 5 O 2813 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.00s 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: 11913 Number of models: 1 Model: "" Number of chains: 10 Chain: "H" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 739 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3011 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3010 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "M" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 765 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "b" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "f" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 782 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "h" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 620 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "k" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 804 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LEU O 22 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU O 22 " occ=0.00 residue: pdb=" N ARG O 23 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG O 23 " occ=0.00 Time building chain proxies: 2.50, per 1000 atoms: 0.21 Number of scatterers: 11913 At special positions: 0 Unit cell: (116.065, 120.24, 104.375, 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 12 16.00 P 292 15.00 O 2813 8.00 N 2205 7.00 C 6591 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: 0.62 Conformation dependent library (CDL) restraints added in 162.5 milliseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1398 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 6 sheets defined 73.0% alpha, 1.6% beta 147 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.503A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.765A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.520A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 57 removed outlier: 3.545A pdb=" N SER M 57 " --> pdb=" O ARG M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 76 Processing helix chain 'M' and resid 85 through 114 removed outlier: 3.555A pdb=" N ALA M 114 " --> pdb=" O CYS M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 131 removed outlier: 3.779A pdb=" N ILE M 124 " --> pdb=" O MET M 120 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 29 removed outlier: 4.088A pdb=" N ILE O 29 " --> pdb=" O ILE O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 30 through 41 Processing helix chain 'O' and resid 50 through 76 removed outlier: 4.044A pdb=" N ASP O 68 " --> pdb=" O ASN O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 93 removed outlier: 3.745A pdb=" N VAL O 86 " --> pdb=" O THR O 82 " (cutoff:3.500A) Processing helix chain 'a' and resid 16 through 22 Processing helix chain 'a' and resid 26 through 37 Processing helix chain 'a' and resid 45 through 72 removed outlier: 4.141A pdb=" N VAL a 49 " --> pdb=" O ALA a 45 " (cutoff:3.500A) Processing helix chain 'a' and resid 79 through 89 removed outlier: 3.666A pdb=" N ASN a 89 " --> pdb=" O LEU a 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 97 Processing helix chain 'b' and resid 34 through 46 removed outlier: 4.186A pdb=" N VAL b 38 " --> pdb=" O TYR b 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 52 through 80 Processing helix chain 'b' and resid 87 through 99 removed outlier: 3.759A pdb=" N LEU b 98 " --> pdb=" O ALA b 94 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU b 99 " --> pdb=" O VAL b 95 " (cutoff:3.500A) Processing helix chain 'b' and resid 100 through 121 removed outlier: 3.884A pdb=" N ALA b 121 " --> pdb=" O LYS b 117 " (cutoff:3.500A) Processing helix chain 'f' and resid 44 through 57 Processing helix chain 'f' and resid 63 through 79 removed outlier: 3.955A pdb=" N PHE f 67 " --> pdb=" O ARG f 63 " (cutoff:3.500A) Processing helix chain 'f' and resid 85 through 114 Processing helix chain 'f' and resid 121 through 131 Processing helix chain 'h' and resid 24 through 29 removed outlier: 3.529A pdb=" N GLN h 27 " --> pdb=" O ASP h 24 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE h 29 " --> pdb=" O ILE h 26 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 42 Processing helix chain 'h' and resid 49 through 76 removed outlier: 3.612A pdb=" N ALA h 76 " --> pdb=" O TYR h 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 82 through 94 removed outlier: 3.823A pdb=" N VAL h 86 " --> pdb=" O THR h 82 " (cutoff:3.500A) Processing helix chain 'k' and resid 16 through 22 removed outlier: 3.776A pdb=" N ARG k 20 " --> pdb=" O THR k 16 " (cutoff:3.500A) Processing helix chain 'k' and resid 26 through 36 removed outlier: 3.995A pdb=" N VAL k 30 " --> pdb=" O PRO k 26 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 74 removed outlier: 4.404A pdb=" N VAL k 49 " --> pdb=" O ALA k 45 " (cutoff:3.500A) Processing helix chain 'k' and resid 79 through 88 Processing helix chain 'k' and resid 90 through 97 Processing sheet with id=AA1, first strand: chain 'H' and resid 50 through 51 removed outlier: 7.857A pdb=" N GLY H 50 " --> pdb=" O ILE k 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'H' and resid 85 through 86 Processing sheet with id=AA3, first strand: chain 'M' and resid 83 through 84 removed outlier: 6.837A pdb=" N ARG M 83 " --> pdb=" O VAL O 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'O' and resid 96 through 97 removed outlier: 6.869A pdb=" N THR O 96 " --> pdb=" O THR k 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'a' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'f' and resid 83 through 84 removed outlier: 7.148A pdb=" N ARG f 83 " --> pdb=" O VAL h 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 390 hydrogen bonds defined for protein. 1164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 354 hydrogen bonds 708 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 0.85 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: 2637 1.34 - 1.46: 4499 1.46 - 1.58: 4978 1.58 - 1.71: 585 1.71 - 1.83: 22 Bond restraints: 12721 Sorted by residual: bond pdb=" C5' DG I -3 " pdb=" C4' DG I -3 " ideal model delta sigma weight residual 1.512 1.537 -0.025 7.00e-03 2.04e+04 1.29e+01 bond pdb=" C3' DC J 15 " pdb=" C2' DC J 15 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.26e+01 bond pdb=" C3' DT J 53 " pdb=" C2' DT J 53 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.23e+01 bond pdb=" C3' DA I 54 " pdb=" C2' DA I 54 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C1' DC I -49 " pdb=" N1 DC I -49 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.09e+01 ... (remaining 12716 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.68: 18243 4.68 - 9.36: 175 9.36 - 14.05: 26 14.05 - 18.73: 3 18.73 - 23.41: 1 Bond angle restraints: 18448 Sorted by residual: angle pdb=" CA PRO a 109 " pdb=" N PRO a 109 " pdb=" CD PRO a 109 " ideal model delta sigma weight residual 112.00 99.08 12.92 1.40e+00 5.10e-01 8.52e+01 angle pdb=" CA LEU f 65 " pdb=" CB LEU f 65 " pdb=" CG LEU f 65 " ideal model delta sigma weight residual 116.30 139.71 -23.41 3.50e+00 8.16e-02 4.47e+01 angle pdb=" O4' DG J 49 " pdb=" C1' DG J 49 " pdb=" N9 DG J 49 " ideal model delta sigma weight residual 108.00 112.62 -4.62 7.00e-01 2.04e+00 4.36e+01 angle pdb=" CA PRO f 43 " pdb=" N PRO f 43 " pdb=" CD PRO f 43 " ideal model delta sigma weight residual 112.00 103.70 8.30 1.40e+00 5.10e-01 3.51e+01 angle pdb=" CA LYS M 64 " pdb=" CB LYS M 64 " pdb=" CG LYS M 64 " ideal model delta sigma weight residual 114.10 125.94 -11.84 2.00e+00 2.50e-01 3.51e+01 ... (remaining 18443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3951 18.00 - 36.00: 1366 36.00 - 54.00: 1251 54.00 - 72.00: 355 72.00 - 90.00: 52 Dihedral angle restraints: 6975 sinusoidal: 4809 harmonic: 2166 Sorted by residual: dihedral pdb=" CA ILE O 50 " pdb=" C ILE O 50 " pdb=" N TYR O 51 " pdb=" CA TYR O 51 " ideal model delta harmonic sigma weight residual 180.00 -150.11 -29.89 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA LEU b 97 " pdb=" C LEU b 97 " pdb=" N LEU b 98 " pdb=" CA LEU b 98 " ideal model delta harmonic sigma weight residual -180.00 -153.98 -26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA LEU a 108 " pdb=" C LEU a 108 " pdb=" N PRO a 109 " pdb=" CA PRO a 109 " ideal model delta harmonic sigma weight residual 180.00 156.51 23.49 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 6972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1835 0.083 - 0.167: 244 0.167 - 0.250: 17 0.250 - 0.334: 4 0.334 - 0.417: 4 Chirality restraints: 2104 Sorted by residual: chirality pdb=" CB VAL H 108 " pdb=" CA VAL H 108 " pdb=" CG1 VAL H 108 " pdb=" CG2 VAL H 108 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CB ILE H 58 " pdb=" CA ILE H 58 " pdb=" CG1 ILE H 58 " pdb=" CG2 ILE H 58 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" CB VAL H 41 " pdb=" CA VAL H 41 " pdb=" CG1 VAL H 41 " pdb=" CG2 VAL H 41 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 2101 not shown) Planarity restraints: 1319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU a 108 " -0.106 5.00e-02 4.00e+02 1.50e-01 3.61e+01 pdb=" N PRO a 109 " 0.259 5.00e-02 4.00e+02 pdb=" CA PRO a 109 " -0.077 5.00e-02 4.00e+02 pdb=" CD PRO a 109 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG f 42 " 0.069 5.00e-02 4.00e+02 9.97e-02 1.59e+01 pdb=" N PRO f 43 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO f 43 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO f 43 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR h 88 " 0.026 2.00e-02 2.50e+03 2.67e-02 1.42e+01 pdb=" CG TYR h 88 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR h 88 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR h 88 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR h 88 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR h 88 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR h 88 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR h 88 " -0.002 2.00e-02 2.50e+03 ... (remaining 1316 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1827 2.77 - 3.30: 10431 3.30 - 3.83: 25130 3.83 - 4.37: 27389 4.37 - 4.90: 37898 Nonbonded interactions: 102675 Sorted by model distance: nonbonded pdb=" O LEU a 55 " pdb=" OG1 THR a 59 " model vdw 2.233 3.040 nonbonded pdb=" OD2 ASP b 65 " pdb=" OH TYR h 98 " model vdw 2.259 3.040 nonbonded pdb=" OP1 DT J 18 " pdb=" NZ LYS M 64 " model vdw 2.267 3.120 nonbonded pdb=" O TYR a 39 " pdb=" OG SER b 75 " model vdw 2.291 3.040 nonbonded pdb=" OD2 ASP H 65 " pdb=" OH TYR O 98 " model vdw 2.294 3.040 ... (remaining 102670 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 'H' and resid 30 through 121) selection = (chain 'b' and (resid 30 through 95 or (resid 96 and (name N or name CA or name \ C or name O or name CB )) or resid 97 through 121)) } ncs_group { reference = (chain 'I' and (resid -73 through -1 or resid 1 through 73)) selection = (chain 'J' and (resid -73 through -1 or resid 1 through 73)) } ncs_group { reference = (chain 'M' and (resid 41 through 48 or (resid 49 and (name N or name CA or name \ C or name O or name CB )) or resid 50 through 99 or (resid 100 and (name N or na \ me CA or name C or name O or name CB )) or resid 101 through 135)) selection = (chain 'f' and (resid 41 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 133 or (resid 134 and (name N or n \ ame CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'O' and (resid 24 through 90 or (resid 91 and (name N or name CA or name \ C or name O or name CB )) or resid 92 through 102)) selection = chain 'h' } ncs_group { reference = (chain 'a' and resid 15 through 118) selection = chain 'k' } 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: 7.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.880 Find NCS groups from input model: 0.190 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.141 12721 Z= 0.591 Angle : 1.329 23.411 18448 Z= 0.935 Chirality : 0.060 0.417 2104 Planarity : 0.011 0.150 1319 Dihedral : 30.772 89.997 5577 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 40.55 % Favored : 59.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.27), residues: 730 helix: -1.65 (0.19), residues: 517 sheet: None (None), residues: 0 loop : -1.38 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG k 71 TYR 0.065 0.005 TYR h 88 PHE 0.056 0.004 PHE O 61 HIS 0.011 0.002 HIS O 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00761 / 0.59 (12721) covalent geometry : angle 1.32877 / 0.94 (18448) hydrogen bonds : bond 0.10322 / 6.67 ( 744) hydrogen bonds : angle 5.25028 / 4.59 ( 1872) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 105 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7442 (mm-30) REVERT: a 112 GLN cc_start: 0.6722 (tp-100) cc_final: 0.6424 (tm-30) REVERT: b 73 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7757 (mm-30) REVERT: b 76 ARG cc_start: 0.8853 (ttm110) cc_final: 0.8527 (ttm110) REVERT: f 90 MET cc_start: 0.8427 (mmm) cc_final: 0.8213 (mmm) REVERT: k 35 ARG cc_start: 0.8779 (tpp80) cc_final: 0.8339 (mpp80) REVERT: k 71 ARG cc_start: 0.8751 (mtm110) cc_final: 0.8224 (mtt90) REVERT: k 91 GLU cc_start: 0.8103 (pp20) cc_final: 0.7599 (pp20) REVERT: k 92 GLU cc_start: 0.7888 (pm20) cc_final: 0.7657 (pm20) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.1327 time to fit residues: 48.5456 Evaluate side-chains 258 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.0270 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0270 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 125 GLN a 73 ASN b 79 HIS ** k 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.098371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.079734 restraints weight = 48858.544| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 3.24 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12721 Z= 0.165 Angle : 0.832 17.218 18448 Z= 0.463 Chirality : 0.051 0.231 2104 Planarity : 0.007 0.073 1319 Dihedral : 32.766 89.968 4127 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.75 % Allowed : 34.85 % Favored : 61.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.28), residues: 730 helix: -0.52 (0.21), residues: 524 sheet: None (None), residues: 0 loop : -1.58 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG k 71 TYR 0.041 0.002 TYR O 88 PHE 0.018 0.002 PHE H 67 HIS 0.019 0.002 HIS O 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.17 (12721) covalent geometry : angle 0.83186 / 0.46 (18448) hydrogen bonds : bond 0.05829 / 3.72 ( 744) hydrogen bonds : angle 4.02657 / 3.50 ( 1872) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 257 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 94 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8490 (pm20) REVERT: b 73 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8164 (mm-30) REVERT: b 76 ARG cc_start: 0.9128 (ttm110) cc_final: 0.8735 (ttm110) REVERT: f 69 ARG cc_start: 0.8139 (mtm180) cc_final: 0.7832 (mtm180) REVERT: h 78 ARG cc_start: 0.6563 (tpt170) cc_final: 0.6360 (tpp80) REVERT: k 35 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8453 (mpp80) REVERT: k 91 GLU cc_start: 0.8341 (pp20) cc_final: 0.7941 (pp20) outliers start: 23 outliers final: 15 residues processed: 266 average time/residue: 0.1251 time to fit residues: 44.3833 Evaluate side-chains 256 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 239 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 91 GLU Chi-restraints excluded: chain b residue 57 SER Chi-restraints excluded: chain b residue 79 HIS Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 58 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 23 optimal weight: 30.0000 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 38 ASN b 79 HIS k 82 HIS k 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.095557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.076959 restraints weight = 50155.340| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 3.21 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12721 Z= 0.190 Angle : 0.799 15.780 18448 Z= 0.451 Chirality : 0.049 0.227 2104 Planarity : 0.006 0.069 1319 Dihedral : 32.687 89.972 4127 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 7.00 % Allowed : 32.90 % Favored : 60.10 % 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: -0.73 (0.29), residues: 730 helix: 0.08 (0.21), residues: 526 sheet: None (None), residues: 0 loop : -1.76 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 52 TYR 0.042 0.003 TYR O 88 PHE 0.017 0.002 PHE O 61 HIS 0.007 0.002 HIS O 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.19 (12721) covalent geometry : angle 0.79889 / 0.45 (18448) hydrogen bonds : bond 0.06138 / 3.97 ( 744) hydrogen bonds : angle 3.90895 / 3.34 ( 1872) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 248 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 40 LYS cc_start: 0.9063 (pttm) cc_final: 0.8684 (pttm) REVERT: M 52 ARG cc_start: 0.8571 (mtm110) cc_final: 0.8332 (mtm110) REVERT: M 94 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8445 (pm20) REVERT: a 65 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8145 (mm) REVERT: b 76 ARG cc_start: 0.9126 (ttm110) cc_final: 0.8698 (ttm110) REVERT: b 113 LYS cc_start: 0.7803 (pptt) cc_final: 0.7585 (pptt) REVERT: k 24 GLN cc_start: 0.6035 (tt0) cc_final: 0.5747 (tp-100) REVERT: k 35 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8394 (mpp80) REVERT: k 91 GLU cc_start: 0.8511 (pp20) cc_final: 0.8029 (pp20) outliers start: 43 outliers final: 31 residues processed: 263 average time/residue: 0.1217 time to fit residues: 43.2636 Evaluate side-chains 269 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 235 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain a residue 107 VAL Chi-restraints excluded: chain b residue 56 MET Chi-restraints excluded: chain b residue 57 SER Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 112 ILE Chi-restraints excluded: chain f residue 117 VAL Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 40 ARG Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 71 THR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 67 optimal weight: 0.5980 chunk 31 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... k 38 ASN k 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.092016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.073295 restraints weight = 50660.541| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 3.13 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12721 Z= 0.238 Angle : 0.832 14.709 18448 Z= 0.466 Chirality : 0.050 0.238 2104 Planarity : 0.007 0.060 1319 Dihedral : 32.776 89.270 4127 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 9.61 % Allowed : 30.62 % Favored : 59.77 % 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: -0.56 (0.29), residues: 730 helix: 0.23 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -1.85 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG h 95 TYR 0.045 0.003 TYR H 80 PHE 0.017 0.003 PHE O 61 HIS 0.008 0.002 HIS h 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.24 (12721) covalent geometry : angle 0.83219 / 0.47 (18448) hydrogen bonds : bond 0.07124 / 4.67 ( 744) hydrogen bonds : angle 4.01217 / 3.42 ( 1872) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 240 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 LYS cc_start: 0.8784 (tppt) cc_final: 0.8553 (tppt) REVERT: H 40 LYS cc_start: 0.9014 (pttm) cc_final: 0.8564 (ptpp) REVERT: M 52 ARG cc_start: 0.8640 (mtm110) cc_final: 0.8088 (mtm110) REVERT: M 105 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7784 (mm-30) REVERT: M 131 ARG cc_start: 0.7839 (ptm160) cc_final: 0.7468 (ptm160) REVERT: a 65 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8235 (mm) REVERT: a 111 ILE cc_start: 0.7062 (mm) cc_final: 0.6837 (mm) REVERT: b 76 ARG cc_start: 0.9079 (ttm110) cc_final: 0.8804 (ttm110) REVERT: h 27 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.6812 (tp-100) REVERT: h 72 TYR cc_start: 0.7771 (OUTLIER) cc_final: 0.7525 (t80) REVERT: k 35 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8365 (mpp80) REVERT: k 61 GLU cc_start: 0.8406 (tp30) cc_final: 0.8124 (tp30) REVERT: k 92 GLU cc_start: 0.8307 (pm20) cc_final: 0.8068 (pm20) outliers start: 59 outliers final: 40 residues processed: 264 average time/residue: 0.1245 time to fit residues: 44.6317 Evaluate side-chains 268 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 224 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain O residue 25 ASN Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 36 LYS Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain a residue 107 VAL Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 56 MET Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 112 ILE Chi-restraints excluded: chain f residue 116 ARG Chi-restraints excluded: chain f residue 117 VAL Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 27 GLN Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 71 THR Chi-restraints excluded: chain h residue 72 TYR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain k residue 93 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 16 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 75 HIS ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 64 ASN ** f 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 24 GLN k 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.093264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.074641 restraints weight = 49808.357| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 3.11 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12721 Z= 0.182 Angle : 0.796 14.336 18448 Z= 0.446 Chirality : 0.048 0.237 2104 Planarity : 0.006 0.058 1319 Dihedral : 32.774 88.680 4127 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 7.33 % Allowed : 32.74 % Favored : 59.93 % 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: -0.27 (0.30), residues: 730 helix: 0.48 (0.21), residues: 531 sheet: None (None), residues: 0 loop : -1.82 (0.41), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG f 83 TYR 0.047 0.003 TYR O 88 PHE 0.014 0.002 PHE O 61 HIS 0.004 0.001 HIS O 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.18 (12721) covalent geometry : angle 0.79593 / 0.45 (18448) hydrogen bonds : bond 0.05870 / 3.78 ( 744) hydrogen bonds : angle 3.82701 / 3.25 ( 1872) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 242 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 LYS cc_start: 0.8842 (tppt) cc_final: 0.8616 (tppt) REVERT: H 102 GLU cc_start: 0.8359 (pp20) cc_final: 0.8124 (pp20) REVERT: M 52 ARG cc_start: 0.8641 (mtm110) cc_final: 0.8420 (mtm110) REVERT: M 105 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7759 (mm-30) REVERT: M 133 GLU cc_start: 0.8001 (mp0) cc_final: 0.7310 (mp0) REVERT: a 65 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8220 (mm) REVERT: b 76 ARG cc_start: 0.9093 (ttm110) cc_final: 0.8786 (ttm110) REVERT: h 72 TYR cc_start: 0.7696 (t80) cc_final: 0.7489 (t80) REVERT: k 23 LEU cc_start: 0.7506 (mt) cc_final: 0.7077 (mp) REVERT: k 24 GLN cc_start: 0.6951 (tp40) cc_final: 0.5985 (tt0) REVERT: k 35 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8424 (mpp80) outliers start: 45 outliers final: 33 residues processed: 259 average time/residue: 0.1246 time to fit residues: 44.0274 Evaluate side-chains 262 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 227 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 75 HIS Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain a residue 107 VAL Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 81 ASP Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 112 ILE Chi-restraints excluded: chain f residue 116 ARG Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 71 THR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 chunk 94 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 23 optimal weight: 30.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 75 HIS a 112 GLN ** f 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.093189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.074480 restraints weight = 49430.701| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 3.08 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12721 Z= 0.184 Angle : 0.807 14.942 18448 Z= 0.447 Chirality : 0.048 0.249 2104 Planarity : 0.006 0.054 1319 Dihedral : 32.706 88.390 4127 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 8.14 % Allowed : 34.04 % Favored : 57.82 % 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: -0.15 (0.30), residues: 730 helix: 0.58 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.84 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG k 71 TYR 0.046 0.003 TYR O 88 PHE 0.011 0.002 PHE O 61 HIS 0.007 0.001 HIS O 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.18 (12721) covalent geometry : angle 0.80679 / 0.45 (18448) hydrogen bonds : bond 0.05892 / 3.79 ( 744) hydrogen bonds : angle 3.78139 / 3.23 ( 1872) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 236 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 LYS cc_start: 0.8833 (tppt) cc_final: 0.8627 (tppt) REVERT: H 102 GLU cc_start: 0.8346 (pp20) cc_final: 0.8102 (pp20) REVERT: M 52 ARG cc_start: 0.8642 (mtm110) cc_final: 0.8119 (mtm110) REVERT: M 105 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7729 (mm-30) REVERT: M 133 GLU cc_start: 0.7956 (mp0) cc_final: 0.7374 (mp0) REVERT: a 65 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8227 (mm) REVERT: b 76 ARG cc_start: 0.9029 (ttm110) cc_final: 0.8753 (ttm110) REVERT: h 72 TYR cc_start: 0.7744 (OUTLIER) cc_final: 0.7454 (t80) REVERT: k 23 LEU cc_start: 0.7604 (mt) cc_final: 0.7260 (mp) REVERT: k 24 GLN cc_start: 0.6933 (tp40) cc_final: 0.5944 (tt0) REVERT: k 35 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8445 (mpp80) outliers start: 50 outliers final: 38 residues processed: 255 average time/residue: 0.1099 time to fit residues: 38.4588 Evaluate side-chains 274 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 233 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain O residue 25 ASN Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 75 HIS Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 36 LYS Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain a residue 107 VAL Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 81 ASP Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 106 ASP Chi-restraints excluded: chain f residue 112 ILE Chi-restraints excluded: chain f residue 116 ARG Chi-restraints excluded: chain f residue 117 VAL Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 71 THR Chi-restraints excluded: chain h residue 72 TYR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 47 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 chunk 80 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 75 HIS a 73 ASN b 64 ASN ** f 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.093398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.074606 restraints weight = 49359.614| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.08 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12721 Z= 0.176 Angle : 0.806 13.779 18448 Z= 0.446 Chirality : 0.048 0.263 2104 Planarity : 0.006 0.054 1319 Dihedral : 32.664 88.490 4127 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 7.00 % Allowed : 34.53 % Favored : 58.47 % 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: -0.11 (0.30), residues: 730 helix: 0.61 (0.21), residues: 530 sheet: None (None), residues: 0 loop : -1.82 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG k 71 TYR 0.046 0.002 TYR O 88 PHE 0.010 0.002 PHE O 61 HIS 0.009 0.001 HIS O 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.18 (12721) covalent geometry : angle 0.80599 / 0.45 (18448) hydrogen bonds : bond 0.05672 / 3.63 ( 744) hydrogen bonds : angle 3.76210 / 3.21 ( 1872) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 245 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.8592 (mmmt) cc_final: 0.8294 (mmtt) REVERT: H 102 GLU cc_start: 0.8314 (pp20) cc_final: 0.8095 (pp20) REVERT: M 52 ARG cc_start: 0.8665 (mtm110) cc_final: 0.8156 (mtm110) REVERT: M 105 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7688 (mm-30) REVERT: M 133 GLU cc_start: 0.7933 (mp0) cc_final: 0.7496 (mp0) REVERT: a 65 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8218 (mm) REVERT: b 76 ARG cc_start: 0.9000 (ttm110) cc_final: 0.8744 (ttm110) REVERT: h 72 TYR cc_start: 0.7760 (OUTLIER) cc_final: 0.7486 (t80) REVERT: k 23 LEU cc_start: 0.7623 (mt) cc_final: 0.7298 (mp) REVERT: k 24 GLN cc_start: 0.6983 (tp40) cc_final: 0.5967 (tt0) REVERT: k 35 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8458 (mpp80) REVERT: k 91 GLU cc_start: 0.8609 (pp20) cc_final: 0.8056 (pp20) outliers start: 43 outliers final: 35 residues processed: 264 average time/residue: 0.1119 time to fit residues: 40.5026 Evaluate side-chains 270 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 232 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain O residue 25 ASN Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 75 HIS Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 36 LYS Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 81 ASP Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 106 ASP Chi-restraints excluded: chain f residue 112 ILE Chi-restraints excluded: chain f residue 116 ARG Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 71 THR Chi-restraints excluded: chain h residue 72 TYR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 57 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 8 optimal weight: 0.6980 chunk 18 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 64 ASN ** f 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 38 ASN k 82 HIS k 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.093826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.075150 restraints weight = 49314.719| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 3.09 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12721 Z= 0.167 Angle : 0.808 13.964 18448 Z= 0.446 Chirality : 0.048 0.236 2104 Planarity : 0.006 0.055 1319 Dihedral : 32.611 88.515 4127 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 6.68 % Allowed : 36.16 % Favored : 57.17 % 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: -0.02 (0.30), residues: 730 helix: 0.68 (0.21), residues: 531 sheet: None (None), residues: 0 loop : -1.80 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG k 71 TYR 0.051 0.002 TYR O 88 PHE 0.009 0.001 PHE O 61 HIS 0.023 0.002 HIS O 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.17 (12721) covalent geometry : angle 0.80787 / 0.45 (18448) hydrogen bonds : bond 0.05470 / 3.48 ( 744) hydrogen bonds : angle 3.74543 / 3.18 ( 1872) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 245 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 102 GLU cc_start: 0.8279 (pp20) cc_final: 0.8063 (pp20) REVERT: M 52 ARG cc_start: 0.8637 (mtm110) cc_final: 0.8140 (mtm110) REVERT: M 105 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7669 (mm-30) REVERT: M 133 GLU cc_start: 0.7876 (mp0) cc_final: 0.7524 (mp0) REVERT: a 65 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8204 (mm) REVERT: b 76 ARG cc_start: 0.8965 (ttm110) cc_final: 0.8715 (ttm110) REVERT: h 72 TYR cc_start: 0.7772 (OUTLIER) cc_final: 0.7496 (t80) REVERT: k 23 LEU cc_start: 0.7612 (mt) cc_final: 0.7297 (mp) REVERT: k 24 GLN cc_start: 0.6982 (tp40) cc_final: 0.5973 (tt0) REVERT: k 35 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8487 (mpp80) outliers start: 41 outliers final: 33 residues processed: 260 average time/residue: 0.1028 time to fit residues: 36.9890 Evaluate side-chains 271 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 235 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain M residue 41 TYR Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 36 LYS Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain a residue 107 VAL Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 81 ASP Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 116 ARG Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 71 THR Chi-restraints excluded: chain h residue 72 TYR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 38 ASN Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 91 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 0.0070 chunk 17 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 26 optimal weight: 20.0000 chunk 84 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 73 ASN ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 64 ASN ** f 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 38 ASN ** k 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.094462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.075795 restraints weight = 48765.231| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 3.04 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12721 Z= 0.166 Angle : 0.821 15.042 18448 Z= 0.450 Chirality : 0.048 0.232 2104 Planarity : 0.006 0.055 1319 Dihedral : 32.542 88.473 4127 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 5.86 % Allowed : 36.97 % Favored : 57.17 % 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: 0.03 (0.30), residues: 730 helix: 0.69 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.70 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG k 71 TYR 0.058 0.003 TYR O 88 PHE 0.009 0.001 PHE O 61 HIS 0.024 0.002 HIS O 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.17 (12721) covalent geometry : angle 0.82126 / 0.45 (18448) hydrogen bonds : bond 0.05280 / 3.34 ( 744) hydrogen bonds : angle 3.70645 / 3.15 ( 1872) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 247 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.8554 (mmmt) cc_final: 0.8249 (mmtt) REVERT: M 52 ARG cc_start: 0.8624 (mtm110) cc_final: 0.8145 (mtm110) REVERT: M 105 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7643 (mm-30) REVERT: M 133 GLU cc_start: 0.7849 (mp0) cc_final: 0.7516 (mp0) REVERT: a 42 ARG cc_start: 0.8162 (mmm-85) cc_final: 0.7788 (mtp85) REVERT: a 65 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8182 (mm) REVERT: b 76 ARG cc_start: 0.9053 (ttm110) cc_final: 0.8696 (ttm110) REVERT: h 72 TYR cc_start: 0.7732 (OUTLIER) cc_final: 0.7446 (t80) REVERT: k 23 LEU cc_start: 0.7600 (mt) cc_final: 0.7233 (mp) REVERT: k 24 GLN cc_start: 0.6982 (tp40) cc_final: 0.6009 (tt0) REVERT: k 35 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8442 (mpp80) outliers start: 36 outliers final: 29 residues processed: 260 average time/residue: 0.1044 time to fit residues: 37.3849 Evaluate side-chains 271 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 239 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain M residue 41 TYR Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 88 TYR Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 36 LYS Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain a residue 107 VAL Chi-restraints excluded: chain b residue 57 SER Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 81 ASP Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 106 ASP Chi-restraints excluded: chain f residue 116 ARG Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 72 TYR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 38 ASN Chi-restraints excluded: chain k residue 58 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 14 optimal weight: 10.9990 chunk 62 optimal weight: 0.9990 chunk 15 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 97 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 72 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 40 optimal weight: 0.0980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 73 ASN ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 64 ASN ** f 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 38 ASN k 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.093427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.074699 restraints weight = 49626.875| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 3.06 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12721 Z= 0.183 Angle : 0.829 14.907 18448 Z= 0.454 Chirality : 0.048 0.236 2104 Planarity : 0.006 0.052 1319 Dihedral : 32.521 88.367 4127 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 5.86 % Allowed : 37.79 % Favored : 56.35 % 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: -0.01 (0.30), residues: 730 helix: 0.68 (0.21), residues: 531 sheet: None (None), residues: 0 loop : -1.76 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG k 71 TYR 0.061 0.003 TYR O 88 PHE 0.024 0.002 PHE b 62 HIS 0.015 0.002 HIS O 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.18 (12721) covalent geometry : angle 0.82904 / 0.45 (18448) hydrogen bonds : bond 0.05613 / 3.61 ( 744) hydrogen bonds : angle 3.77646 / 3.20 ( 1872) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 239 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.8595 (mmmt) cc_final: 0.8258 (mmtt) REVERT: M 105 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7680 (mm-30) REVERT: M 133 GLU cc_start: 0.7954 (mp0) cc_final: 0.7632 (mp0) REVERT: a 42 ARG cc_start: 0.8222 (mmm-85) cc_final: 0.7840 (ttp80) REVERT: a 65 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8246 (mm) REVERT: b 76 ARG cc_start: 0.9089 (ttm110) cc_final: 0.8704 (ttm110) REVERT: h 66 ILE cc_start: 0.9031 (pt) cc_final: 0.8581 (mt) REVERT: h 72 TYR cc_start: 0.7855 (OUTLIER) cc_final: 0.7562 (t80) REVERT: k 23 LEU cc_start: 0.7683 (mt) cc_final: 0.7311 (mp) REVERT: k 24 GLN cc_start: 0.7129 (tp40) cc_final: 0.6076 (tt0) REVERT: k 35 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8452 (mpp80) outliers start: 36 outliers final: 31 residues processed: 252 average time/residue: 0.1063 time to fit residues: 36.9780 Evaluate side-chains 270 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 236 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain M residue 41 TYR Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 88 TYR Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 36 LYS Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain a residue 107 VAL Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 81 ASP Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 106 ASP Chi-restraints excluded: chain f residue 116 ARG Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 72 TYR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 38 ASN Chi-restraints excluded: chain k residue 58 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 70 optimal weight: 0.2980 chunk 41 optimal weight: 0.9980 chunk 26 optimal weight: 20.0000 chunk 73 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 93 GLN ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 64 ASN ** f 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 38 ASN k 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.094339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.075508 restraints weight = 49244.145| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 3.05 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12721 Z= 0.166 Angle : 0.828 14.851 18448 Z= 0.452 Chirality : 0.048 0.233 2104 Planarity : 0.006 0.051 1319 Dihedral : 32.509 88.726 4127 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 6.19 % Allowed : 37.13 % Favored : 56.68 % 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: -0.02 (0.30), residues: 730 helix: 0.66 (0.21), residues: 531 sheet: None (None), residues: 0 loop : -1.76 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG k 71 TYR 0.059 0.003 TYR O 88 PHE 0.024 0.002 PHE b 62 HIS 0.017 0.002 HIS O 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.17 (12721) covalent geometry : angle 0.82842 / 0.45 (18448) hydrogen bonds : bond 0.05276 / 3.35 ( 744) hydrogen bonds : angle 3.71291 / 3.16 ( 1872) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2213.21 seconds wall clock time: 38 minutes 43.02 seconds (2323.02 seconds total)