Starting phenix.real_space_refine on Fri Jul 3 02:46:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8euj_28614/07_2026/8euj_28614_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8euj_28614/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8euj_28614/07_2026/8euj_28614_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8euj_28614/07_2026/8euj_28614_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8euj_28614/07_2026/8euj_28614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8euj_28614/07_2026/8euj_28614.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.64, per 1000 atoms: 0.22 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: 0.77 Conformation dependent library (CDL) restraints added in 244.3 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: 1.85 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: 2.34 Time building geometry restraints manager: 1.10 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: 11.040 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.820 Find NCS groups from input model: 0.140 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: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.480 ------------------------------------------------------------------------------- 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= 0.590 Angle : 1.322 23.411 18448 Z= 0.928 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 1.32247 / 0.93 (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 : 0.244 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: 0.8528 (ttm110) REVERT: f 90 MET cc_start: 0.8427 (mmm) cc_final: 0.8214 (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: 0.1246 time to fit residues: 45.4967 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 : 0.294 ------------------------------------------------------------------------------- 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: 7.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 125 GLN ** a 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 79 HIS k 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.097745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.079101 restraints weight = 48998.251| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 3.22 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12721 Z= 0.171 Angle : 0.825 16.967 18448 Z= 0.460 Chirality : 0.051 0.226 2104 Planarity : 0.007 0.074 1319 Dihedral : 32.878 89.761 4127 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.07 % Allowed : 34.20 % Favored : 61.73 % 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: -1.34 (0.28), residues: 730 helix: -0.53 (0.20), residues: 526 sheet: None (None), residues: 0 loop : -1.50 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG k 71 TYR 0.045 0.003 TYR O 88 PHE 0.012 0.001 PHE a 25 HIS 0.010 0.001 HIS O 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.17 (12721) covalent geometry : angle 0.82475 / 0.46 (18448) hydrogen bonds : bond 0.05913 / 3.78 ( 744) hydrogen bonds : angle 4.01139 / 3.48 ( 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: 25 poor density : 255 time to evaluate : 0.301 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: H 39 TYR cc_start: 0.7974 (t80) cc_final: 0.7771 (t80) REVERT: M 94 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8499 (pm20) REVERT: a 33 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9086 (mm) REVERT: b 76 ARG cc_start: 0.9124 (ttm110) cc_final: 0.8737 (ttm110) REVERT: k 35 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8428 (mpp80) REVERT: k 91 GLU cc_start: 0.8342 (pp20) cc_final: 0.7955 (pp20) outliers start: 25 outliers final: 17 residues processed: 264 average time/residue: 0.1323 time to fit residues: 46.6847 Evaluate side-chains 258 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 238 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 33 LEU 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 58 ILE 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 117 VAL 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: 0.4980 chunk 84 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 56 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 79 HIS ** f 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 82 HIS k 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.096266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.077653 restraints weight = 50215.230| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 3.23 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1593 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= 0.176 Angle : 0.782 16.048 18448 Z= 0.443 Chirality : 0.048 0.222 2104 Planarity : 0.006 0.069 1319 Dihedral : 32.760 89.695 4127 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 6.84 % Allowed : 32.57 % Favored : 60.59 % 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: -0.67 (0.29), residues: 730 helix: 0.10 (0.21), residues: 525 sheet: None (None), residues: 0 loop : -1.67 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 52 TYR 0.043 0.002 TYR O 88 PHE 0.017 0.002 PHE O 61 HIS 0.007 0.001 HIS O 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.18 (12721) covalent geometry : angle 0.78173 / 0.44 (18448) hydrogen bonds : bond 0.05780 / 3.71 ( 744) hydrogen bonds : angle 3.86478 / 3.30 ( 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 288 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 246 time to evaluate : 0.307 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: symmetry clash REVERT: H 39 TYR cc_start: 0.8011 (t80) cc_final: 0.7736 (t80) REVERT: H 40 LYS cc_start: 0.9051 (pttm) cc_final: 0.8685 (pttm) REVERT: M 52 ARG cc_start: 0.8559 (mtm110) cc_final: 0.8337 (mtm110) REVERT: M 94 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8428 (pm20) REVERT: a 33 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9062 (mm) REVERT: a 65 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8132 (mm) REVERT: b 76 ARG cc_start: 0.9062 (ttm110) cc_final: 0.8671 (ttm110) REVERT: b 113 LYS cc_start: 0.7783 (pptt) cc_final: 0.7570 (pptt) REVERT: k 24 GLN cc_start: 0.5890 (tt0) cc_final: 0.5633 (tp-100) REVERT: k 35 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8399 (mpp80) REVERT: k 61 GLU cc_start: 0.8190 (tp30) cc_final: 0.7964 (tp30) REVERT: k 91 GLU cc_start: 0.8476 (pp20) cc_final: 0.8005 (pp20) outliers start: 42 outliers final: 30 residues processed: 260 average time/residue: 0.1303 time to fit residues: 45.4668 Evaluate side-chains 268 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 234 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 33 LEU 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 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: 2.9990 chunk 22 optimal weight: 20.0000 chunk 83 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 31 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 38 ASN a 73 ASN 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 = 0.4083 r_free = 0.4083 target = 0.093285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.074566 restraints weight = 50489.755| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 3.17 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12721 Z= 0.213 Angle : 0.795 15.247 18448 Z= 0.449 Chirality : 0.049 0.229 2104 Planarity : 0.006 0.064 1319 Dihedral : 32.767 88.711 4127 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 8.31 % Allowed : 31.43 % Favored : 60.26 % 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: -0.31 (0.30), residues: 730 helix: 0.37 (0.21), residues: 531 sheet: None (None), residues: 0 loop : -1.58 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG f 83 TYR 0.044 0.003 TYR H 80 PHE 0.017 0.002 PHE O 61 HIS 0.006 0.002 HIS h 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.21 (12721) covalent geometry : angle 0.79468 / 0.45 (18448) hydrogen bonds : bond 0.06500 / 4.23 ( 744) hydrogen bonds : angle 3.90218 / 3.32 ( 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 296 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 245 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 LYS cc_start: 0.8837 (tptt) cc_final: 0.8530 (tppt) REVERT: H 40 LYS cc_start: 0.9040 (pttm) cc_final: 0.8591 (ptpp) REVERT: M 52 ARG cc_start: 0.8602 (mtm110) cc_final: 0.8383 (mtm110) REVERT: M 105 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7788 (mm-30) REVERT: a 33 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9014 (mm) REVERT: a 65 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8207 (mm) REVERT: b 76 ARG cc_start: 0.9108 (ttm110) cc_final: 0.8822 (ttm110) REVERT: h 72 TYR cc_start: 0.7742 (t80) cc_final: 0.7474 (t80) REVERT: k 35 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8393 (mpp80) REVERT: k 92 GLU cc_start: 0.8326 (pm20) cc_final: 0.8046 (pm20) outliers start: 51 outliers final: 38 residues processed: 264 average time/residue: 0.1212 time to fit residues: 43.2087 Evaluate side-chains 271 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 230 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 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 118 THR 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 96 THR Chi-restraints excluded: chain a residue 33 LEU 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 b residue 49 THR Chi-restraints excluded: chain b residue 56 MET Chi-restraints excluded: chain b residue 57 SER 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 16 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 28 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 75 HIS a 38 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 = 0.4110 r_free = 0.4110 target = 0.094940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.076170 restraints weight = 49729.186| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 3.17 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12721 Z= 0.165 Angle : 0.770 15.136 18448 Z= 0.435 Chirality : 0.047 0.242 2104 Planarity : 0.006 0.064 1319 Dihedral : 32.722 88.487 4127 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 7.17 % Allowed : 33.06 % 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: -0.10 (0.30), residues: 730 helix: 0.54 (0.21), residues: 531 sheet: None (None), residues: 0 loop : -1.55 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG h 35 TYR 0.046 0.003 TYR O 88 PHE 0.013 0.002 PHE O 61 HIS 0.003 0.001 HIS h 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.16 (12721) covalent geometry : angle 0.76961 / 0.44 (18448) hydrogen bonds : bond 0.05399 / 3.44 ( 744) hydrogen bonds : angle 3.72400 / 3.16 ( 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 293 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 249 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 LYS cc_start: 0.8818 (tptt) cc_final: 0.8506 (tppt) REVERT: H 102 GLU cc_start: 0.8329 (pp20) cc_final: 0.8025 (pp20) REVERT: M 52 ARG cc_start: 0.8609 (mtm110) cc_final: 0.8400 (mtm110) REVERT: M 105 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7679 (mm-30) REVERT: a 33 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9018 (mm) REVERT: a 65 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8196 (mm) REVERT: b 76 ARG cc_start: 0.9073 (ttm110) cc_final: 0.8697 (ttm110) REVERT: f 90 MET cc_start: 0.8364 (mmp) cc_final: 0.8150 (mmm) REVERT: h 72 TYR cc_start: 0.7675 (OUTLIER) cc_final: 0.7385 (t80) REVERT: k 23 LEU cc_start: 0.7357 (mt) cc_final: 0.6894 (mp) REVERT: k 24 GLN cc_start: 0.6789 (tp40) cc_final: 0.5828 (tt0) REVERT: k 35 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8380 (mpp80) outliers start: 44 outliers final: 31 residues processed: 265 average time/residue: 0.1185 time to fit residues: 42.8886 Evaluate side-chains 271 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 118 THR 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 33 LEU Chi-restraints excluded: chain a residue 36 LYS Chi-restraints excluded: chain a residue 38 ASN 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 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 48 LEU Chi-restraints excluded: chain f residue 81 ASP Chi-restraints excluded: chain f residue 92 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 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 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: 0.5980 chunk 13 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 23 optimal weight: 30.0000 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 73 ASN ** f 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 38 ASN k 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.094174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.075433 restraints weight = 49973.505| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 3.15 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2362 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= 0.180 Angle : 0.790 15.059 18448 Z= 0.441 Chirality : 0.048 0.257 2104 Planarity : 0.006 0.061 1319 Dihedral : 32.673 88.018 4127 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 7.65 % Allowed : 33.71 % Favored : 58.63 % 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: -0.08 (0.30), residues: 730 helix: 0.57 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.61 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG k 71 TYR 0.050 0.003 TYR O 88 PHE 0.011 0.002 PHE O 61 HIS 0.011 0.001 HIS O 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.18 (12721) covalent geometry : angle 0.79039 / 0.44 (18448) hydrogen bonds : bond 0.05638 / 3.61 ( 744) hydrogen bonds : angle 3.75956 / 3.18 ( 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 292 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 245 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 LYS cc_start: 0.8833 (tptt) cc_final: 0.8550 (tppt) REVERT: H 102 GLU cc_start: 0.8342 (pp20) cc_final: 0.8039 (pp20) REVERT: M 52 ARG cc_start: 0.8621 (mtm110) cc_final: 0.8116 (mtm110) REVERT: M 105 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7708 (mm-30) REVERT: a 33 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8960 (mm) REVERT: a 65 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8223 (mm) REVERT: b 76 ARG cc_start: 0.9024 (ttm110) cc_final: 0.8583 (ttm110) REVERT: f 59 GLU cc_start: 0.8309 (tp30) cc_final: 0.8040 (tp30) REVERT: h 72 TYR cc_start: 0.7767 (OUTLIER) cc_final: 0.7487 (t80) REVERT: k 23 LEU cc_start: 0.7459 (mt) cc_final: 0.7019 (mp) REVERT: k 24 GLN cc_start: 0.6747 (tp40) cc_final: 0.5863 (tt0) REVERT: k 35 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8413 (mpp80) outliers start: 47 outliers final: 36 residues processed: 261 average time/residue: 0.1100 time to fit residues: 39.2105 Evaluate side-chains 275 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 235 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 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 33 LEU Chi-restraints excluded: chain a residue 36 LYS Chi-restraints excluded: chain a residue 38 ASN 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 56 MET 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 92 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 47 optimal weight: 0.9990 chunk 9 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 80 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 38 ASN ** f 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 93 GLN 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 = 0.4098 r_free = 0.4098 target = 0.094114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.075319 restraints weight = 49231.195| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 3.09 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12721 Z= 0.173 Angle : 0.788 14.475 18448 Z= 0.440 Chirality : 0.047 0.236 2104 Planarity : 0.006 0.061 1319 Dihedral : 32.657 88.036 4127 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 7.98 % Allowed : 33.71 % Favored : 58.31 % 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: 0.59 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.56 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG h 78 TYR 0.059 0.003 TYR O 88 PHE 0.010 0.001 PHE O 61 HIS 0.008 0.001 HIS O 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 (12721) covalent geometry : angle 0.78775 / 0.44 (18448) hydrogen bonds : bond 0.05555 / 3.54 ( 744) hydrogen bonds : angle 3.75463 / 3.17 ( 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 296 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 247 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 LYS cc_start: 0.8842 (tptt) cc_final: 0.8567 (tppt) REVERT: H 98 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.7927 (tt) REVERT: H 102 GLU cc_start: 0.8354 (pp20) cc_final: 0.8071 (pp20) REVERT: M 52 ARG cc_start: 0.8621 (mtm110) cc_final: 0.8127 (mtm110) REVERT: M 105 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7701 (mm-30) REVERT: a 33 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8968 (mm) REVERT: a 65 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8165 (mm) REVERT: b 76 ARG cc_start: 0.9104 (ttm110) cc_final: 0.8681 (ttm110) REVERT: h 72 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.7503 (t80) REVERT: k 23 LEU cc_start: 0.7533 (mt) cc_final: 0.7128 (mp) REVERT: k 24 GLN cc_start: 0.6783 (tp40) cc_final: 0.5848 (tt0) REVERT: k 35 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8395 (mpp80) REVERT: k 91 GLU cc_start: 0.8579 (pp20) cc_final: 0.8048 (pp20) outliers start: 49 outliers final: 35 residues processed: 266 average time/residue: 0.1147 time to fit residues: 41.4898 Evaluate side-chains 278 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 238 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 98 LEU 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 118 THR 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 88 TYR Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 36 LYS Chi-restraints excluded: chain a residue 38 ASN 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 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 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 38 ASN 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: 1.9990 chunk 81 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 8 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 73 ASN ** f 55 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 = 0.093987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.075271 restraints weight = 49450.653| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 3.09 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12721 Z= 0.178 Angle : 0.798 14.186 18448 Z= 0.443 Chirality : 0.047 0.236 2104 Planarity : 0.006 0.066 1319 Dihedral : 32.638 87.944 4127 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 7.98 % Allowed : 34.53 % Favored : 57.49 % 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: -0.00 (0.30), residues: 730 helix: 0.63 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.61 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG k 71 TYR 0.057 0.003 TYR O 88 PHE 0.010 0.002 PHE O 61 HIS 0.007 0.001 HIS O 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.18 (12721) covalent geometry : angle 0.79848 / 0.44 (18448) hydrogen bonds : bond 0.05556 / 3.55 ( 744) hydrogen bonds : angle 3.75327 / 3.16 ( 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 292 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 243 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 LYS cc_start: 0.8869 (tptt) cc_final: 0.8548 (tppt) REVERT: H 98 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.7998 (tt) REVERT: H 102 GLU cc_start: 0.8350 (pp20) cc_final: 0.8062 (pp20) REVERT: M 52 ARG cc_start: 0.8629 (mtm110) cc_final: 0.8120 (mtm110) REVERT: M 105 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7711 (mm-30) REVERT: a 33 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8965 (mm) REVERT: a 65 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8186 (mm) REVERT: b 76 ARG cc_start: 0.9078 (ttm110) cc_final: 0.8661 (ttm110) REVERT: b 113 LYS cc_start: 0.7709 (pptt) cc_final: 0.7493 (pptt) REVERT: h 72 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.7593 (t80) REVERT: k 23 LEU cc_start: 0.7603 (mt) cc_final: 0.7251 (mp) REVERT: k 24 GLN cc_start: 0.6890 (tp40) cc_final: 0.5865 (tt0) REVERT: k 35 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8429 (mpp80) outliers start: 49 outliers final: 36 residues processed: 262 average time/residue: 0.1090 time to fit residues: 39.4081 Evaluate side-chains 276 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 235 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 98 LEU 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 88 TYR Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 36 LYS Chi-restraints excluded: chain a residue 38 ASN 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 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 Chi-restraints excluded: chain k residue 101 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 91 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 26 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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** 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 = 0.4090 r_free = 0.4090 target = 0.093622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.074821 restraints weight = 49189.760| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 3.08 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12721 Z= 0.184 Angle : 0.805 13.943 18448 Z= 0.447 Chirality : 0.048 0.237 2104 Planarity : 0.006 0.067 1319 Dihedral : 32.627 87.950 4127 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 7.49 % Allowed : 35.02 % Favored : 57.49 % 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: 0.04 (0.30), residues: 730 helix: 0.63 (0.22), residues: 535 sheet: None (None), residues: 0 loop : -1.51 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG k 71 TYR 0.056 0.003 TYR O 88 PHE 0.020 0.002 PHE b 62 HIS 0.008 0.001 HIS O 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.18 (12721) covalent geometry : angle 0.80535 / 0.45 (18448) hydrogen bonds : bond 0.05656 / 3.62 ( 744) hydrogen bonds : angle 3.77343 / 3.20 ( 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 285 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 239 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 98 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8021 (tt) REVERT: H 102 GLU cc_start: 0.8354 (pp20) cc_final: 0.8081 (pp20) REVERT: M 52 ARG cc_start: 0.8634 (mtm110) cc_final: 0.8123 (mtm110) REVERT: M 105 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7691 (mm-30) REVERT: a 33 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8951 (mm) REVERT: a 65 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8196 (mm) REVERT: b 76 ARG cc_start: 0.9085 (ttm110) cc_final: 0.8683 (ttm110) REVERT: b 113 LYS cc_start: 0.7758 (pptt) cc_final: 0.7522 (pptt) REVERT: h 72 TYR cc_start: 0.7836 (OUTLIER) cc_final: 0.7585 (t80) REVERT: k 23 LEU cc_start: 0.7657 (mt) cc_final: 0.7314 (mp) REVERT: k 24 GLN cc_start: 0.6989 (tp40) cc_final: 0.5945 (tt0) REVERT: k 32 ARG cc_start: 0.8608 (tmm-80) cc_final: 0.8052 (tmm-80) REVERT: k 35 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8432 (mpp80) outliers start: 46 outliers final: 38 residues processed: 255 average time/residue: 0.1100 time to fit residues: 38.7827 Evaluate side-chains 278 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 235 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 98 LEU 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 88 TYR Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 33 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 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 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 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 Chi-restraints excluded: chain k residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 14 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 15 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 97 optimal weight: 0.0770 chunk 50 optimal weight: 0.7980 chunk 24 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 38 ASN a 73 ASN ** f 55 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 = 0.4111 r_free = 0.4111 target = 0.094991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.076272 restraints weight = 49215.652| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 3.11 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12721 Z= 0.164 Angle : 0.813 14.085 18448 Z= 0.447 Chirality : 0.047 0.242 2104 Planarity : 0.006 0.065 1319 Dihedral : 32.583 88.137 4127 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 6.35 % Allowed : 36.81 % Favored : 56.84 % 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: 0.09 (0.30), residues: 730 helix: 0.66 (0.22), residues: 535 sheet: None (None), residues: 0 loop : -1.46 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG k 71 TYR 0.055 0.003 TYR O 88 PHE 0.021 0.002 PHE b 62 HIS 0.004 0.001 HIS h 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (12721) covalent geometry : angle 0.81300 / 0.45 (18448) hydrogen bonds : bond 0.05256 / 3.32 ( 744) hydrogen bonds : angle 3.69617 / 3.12 ( 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 288 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 249 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 92 GLN cc_start: 0.8535 (tp40) cc_final: 0.8251 (tp40) REVERT: H 98 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8034 (tt) REVERT: H 102 GLU cc_start: 0.8311 (pp20) cc_final: 0.8044 (pp20) REVERT: M 52 ARG cc_start: 0.8594 (mtm110) cc_final: 0.8128 (mtm110) REVERT: M 105 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7642 (mm-30) REVERT: a 33 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8936 (mm) REVERT: a 42 ARG cc_start: 0.8158 (mmm-85) cc_final: 0.7624 (ttp80) REVERT: a 65 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8221 (mm) REVERT: b 76 ARG cc_start: 0.9051 (ttm110) cc_final: 0.8683 (ttm110) REVERT: b 113 LYS cc_start: 0.7733 (pptt) cc_final: 0.7501 (pptt) REVERT: h 72 TYR cc_start: 0.7820 (OUTLIER) cc_final: 0.7587 (t80) REVERT: k 23 LEU cc_start: 0.7566 (mt) cc_final: 0.7181 (mp) REVERT: k 24 GLN cc_start: 0.7067 (tp40) cc_final: 0.6006 (tt0) REVERT: k 35 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8428 (mpp80) outliers start: 39 outliers final: 29 residues processed: 263 average time/residue: 0.1154 time to fit residues: 41.5877 Evaluate side-chains 274 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 240 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 98 LEU 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 O residue 50 ILE Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 36 LYS Chi-restraints excluded: chain a residue 38 ASN 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 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 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 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 Chi-restraints excluded: chain k residue 101 THR 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: 2.9990 chunk 70 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 26 optimal weight: 20.0000 chunk 73 optimal weight: 0.0040 chunk 0 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 75 HIS O 93 GLN b 64 ASN b 79 HIS ** f 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 38 ASN k 82 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.095216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.076242 restraints weight = 49093.439| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 3.08 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2769 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= 0.165 Angle : 0.812 14.257 18448 Z= 0.447 Chirality : 0.048 0.237 2104 Planarity : 0.006 0.064 1319 Dihedral : 32.547 88.027 4127 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 6.84 % Allowed : 36.97 % Favored : 56.19 % 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: 0.08 (0.30), residues: 730 helix: 0.68 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.54 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG k 71 TYR 0.054 0.003 TYR O 88 PHE 0.025 0.002 PHE b 62 HIS 0.009 0.001 HIS O 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.16 (12721) covalent geometry : angle 0.81225 / 0.45 (18448) hydrogen bonds : bond 0.05252 / 3.33 ( 744) hydrogen bonds : angle 3.67952 / 3.12 ( 1872) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2222.81 seconds wall clock time: 39 minutes 4.44 seconds (2344.44 seconds total)