Starting phenix.real_space_refine on Wed Aug 5 22:21:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jl9_36389/08_2026/8jl9_36389.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jl9_36389/08_2026/8jl9_36389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jl9_36389/08_2026/8jl9_36389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jl9_36389/08_2026/8jl9_36389.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jl9_36389/08_2026/8jl9_36389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jl9_36389/08_2026/8jl9_36389.map" } resolution = 2.65 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= 0.002 sd= 0.033 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 310 5.49 5 S 14 5.16 5 C 6763 2.51 5 N 2312 2.21 5 O 2915 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12314 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3178 Classifications: {'DNA': 155} Link IDs: {'rna3p': 154} Chain: "J" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3177 Classifications: {'DNA': 155} Link IDs: {'rna3p': 154} Time building chain proxies: 2.75, per 1000 atoms: 0.22 Number of scatterers: 12314 At special positions: 0 Unit cell: (74.2, 120.84, 129.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 310 15.00 O 2915 8.00 N 2312 7.00 C 6763 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: 0.95 Conformation dependent library (CDL) restraints added in 348.5 milliseconds 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 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: 36 helices and 10 sheets defined 73.4% alpha, 3.2% beta 155 base pairs and 283 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.932A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.656A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.481A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.504A pdb=" N LEU C 116 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.973A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.671A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.474A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.897A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.277A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.329A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.914A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.126A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 412 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 398 hydrogen bonds 796 hydrogen bond angles 0 basepair planarities 155 basepair parallelities 283 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2146 1.33 - 1.45: 4427 1.45 - 1.57: 5950 1.57 - 1.69: 619 1.69 - 1.81: 24 Bond restraints: 13166 Sorted by residual: bond pdb=" C SER D 32 " pdb=" N ARG D 33 " ideal model delta sigma weight residual 1.330 1.257 0.073 1.39e-02 5.18e+03 2.73e+01 bond pdb=" C3' DT I -71 " pdb=" C2' DT I -71 " ideal model delta sigma weight residual 1.516 1.549 -0.033 8.00e-03 1.56e+04 1.73e+01 bond pdb=" C3' DT I -76 " pdb=" C2' DT I -76 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.55e+01 bond pdb=" C3' DG I 77 " pdb=" C2' DG I 77 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.54e+01 bond pdb=" C3' DC I -63 " pdb=" C2' DC I -63 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.43e+01 ... (remaining 13161 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 18064 2.25 - 4.50: 978 4.50 - 6.75: 68 6.75 - 9.00: 1 9.00 - 11.25: 1 Bond angle restraints: 19112 Sorted by residual: angle pdb=" O4' DA J 71 " pdb=" C1' DA J 71 " pdb=" N9 DA J 71 " ideal model delta sigma weight residual 108.00 112.55 -4.55 7.00e-01 2.04e+00 4.22e+01 angle pdb=" O4' DA I 71 " pdb=" C1' DA I 71 " pdb=" N9 DA I 71 " ideal model delta sigma weight residual 108.00 112.08 -4.08 7.00e-01 2.04e+00 3.39e+01 angle pdb=" O4' DA J 16 " pdb=" C1' DA J 16 " pdb=" N9 DA J 16 " ideal model delta sigma weight residual 108.00 112.05 -4.05 7.00e-01 2.04e+00 3.35e+01 angle pdb=" C SER D 32 " pdb=" CA SER D 32 " pdb=" CB SER D 32 " ideal model delta sigma weight residual 110.42 121.67 -11.25 1.99e+00 2.53e-01 3.20e+01 angle pdb=" O4' DT I -76 " pdb=" C1' DT I -76 " pdb=" N1 DT I -76 " ideal model delta sigma weight residual 108.00 104.14 3.86 7.00e-01 2.04e+00 3.04e+01 ... (remaining 19107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.16: 5357 32.16 - 64.31: 1688 64.31 - 96.47: 53 96.47 - 128.63: 0 128.63 - 160.79: 2 Dihedral angle restraints: 7100 sinusoidal: 4927 harmonic: 2173 Sorted by residual: dihedral pdb=" C SER D 32 " pdb=" N SER D 32 " pdb=" CA SER D 32 " pdb=" CB SER D 32 " ideal model delta harmonic sigma weight residual -122.60 -140.37 17.77 0 2.50e+00 1.60e-01 5.05e+01 dihedral pdb=" N SER D 32 " pdb=" C SER D 32 " pdb=" CA SER D 32 " pdb=" CB SER D 32 " ideal model delta harmonic sigma weight residual 122.80 135.82 -13.02 0 2.50e+00 1.60e-01 2.71e+01 dihedral pdb=" CA ARG D 33 " pdb=" C ARG D 33 " pdb=" N LYS D 34 " pdb=" CA LYS D 34 " ideal model delta harmonic sigma weight residual 180.00 159.72 20.28 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 7097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 1994 0.119 - 0.238: 170 0.238 - 0.357: 6 0.357 - 0.476: 0 0.476 - 0.595: 1 Chirality restraints: 2171 Sorted by residual: chirality pdb=" CA SER D 32 " pdb=" N SER D 32 " pdb=" C SER D 32 " pdb=" CB SER D 32 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.60 2.00e-01 2.50e+01 8.86e+00 chirality pdb=" CA PRO B 32 " pdb=" N PRO B 32 " pdb=" C PRO B 32 " pdb=" CB PRO B 32 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA PRO F 32 " pdb=" N PRO F 32 " pdb=" C PRO F 32 " pdb=" CB PRO F 32 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 2168 not shown) Planarity restraints: 1347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 40 " -0.099 2.00e-02 2.50e+03 5.09e-02 5.18e+01 pdb=" CG TYR D 40 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR D 40 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR D 40 " 0.057 2.00e-02 2.50e+03 pdb=" CE1 TYR D 40 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR D 40 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 40 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR D 40 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 17 " -0.531 9.50e-02 1.11e+02 2.38e-01 3.48e+01 pdb=" NE ARG G 17 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG G 17 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG G 17 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG G 17 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I -76 " 0.052 2.00e-02 2.50e+03 2.80e-02 1.96e+01 pdb=" N1 DT I -76 " -0.070 2.00e-02 2.50e+03 pdb=" C2 DT I -76 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DT I -76 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT I -76 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DT I -76 " 0.008 2.00e-02 2.50e+03 pdb=" O4 DT I -76 " 0.012 2.00e-02 2.50e+03 pdb=" C5 DT I -76 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT I -76 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DT I -76 " -0.005 2.00e-02 2.50e+03 ... (remaining 1344 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 8 2.47 - 3.08: 7511 3.08 - 3.69: 20503 3.69 - 4.29: 32533 4.29 - 4.90: 46271 Nonbonded interactions: 106826 Sorted by model distance: nonbonded pdb=" OD2 ASP F 68 " pdb=" NH1 ARG F 92 " model vdw 1.865 3.120 nonbonded pdb=" NH2 ARG F 92 " pdb=" O LEU H 100 " model vdw 2.337 3.120 nonbonded pdb=" O HIS F 75 " pdb=" NH1 ARG H 92 " model vdw 2.399 3.120 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.403 3.040 nonbonded pdb=" O ASN D 67 " pdb=" OE1 GLU D 71 " model vdw 2.403 3.040 ... (remaining 106821 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 133) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid -77 through -1 or resid 1 through 77)) selection = (chain 'J' and (resid -77 through -1 or resid 1 through 77)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 0.040 Set scattering table: 0.030 Process input model: 13.300 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 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 : 0.007 0.111 13166 Z= 0.595 Angle : 0.999 11.254 19112 Z= 0.826 Chirality : 0.063 0.595 2171 Planarity : 0.012 0.238 1347 Dihedral : 28.861 160.785 5702 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Cbeta Deviations : 0.14 % 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: 0.24 (0.27), residues: 737 helix: 0.48 (0.20), residues: 532 sheet: None (None), residues: 0 loop : -0.40 (0.37), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 63 TYR 0.099 0.004 TYR D 40 PHE 0.012 0.002 PHE A 84 HIS 0.006 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00713 / 0.60 (13166) covalent geometry : angle 0.99883 / 0.83 (19112) hydrogen bonds : bond 0.10462 / 7.13 ( 810) hydrogen bonds : angle 4.26159 / 3.14 ( 2008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.309 Fit side-chains REVERT: A 60 LEU cc_start: 0.7254 (mt) cc_final: 0.7029 (mt) REVERT: A 106 ASP cc_start: 0.6034 (m-30) cc_final: 0.5524 (m-30) REVERT: A 120 MET cc_start: 0.6701 (mtt) cc_final: 0.6388 (mtm) REVERT: A 123 ASP cc_start: 0.6922 (m-30) cc_final: 0.6526 (m-30) REVERT: A 128 ARG cc_start: 0.6531 (mtp180) cc_final: 0.6273 (mmm160) REVERT: B 79 LYS cc_start: 0.6802 (mmtm) cc_final: 0.6554 (mmtp) REVERT: B 84 MET cc_start: 0.6224 (mmm) cc_final: 0.5991 (mmp) REVERT: C 104 GLN cc_start: 0.7350 (tp40) cc_final: 0.6913 (mp10) REVERT: E 53 ARG cc_start: 0.6337 (ttp-110) cc_final: 0.5974 (ttp-110) REVERT: E 120 MET cc_start: 0.6824 (mtt) cc_final: 0.6491 (mtm) REVERT: E 122 LYS cc_start: 0.6425 (pttt) cc_final: 0.6153 (pttp) REVERT: G 40 SER cc_start: 0.7793 (p) cc_final: 0.7524 (p) REVERT: G 42 ARG cc_start: 0.5862 (mtp85) cc_final: 0.5392 (mtp85) REVERT: G 89 ASN cc_start: 0.7383 (m-40) cc_final: 0.6977 (m110) REVERT: H 71 GLU cc_start: 0.6421 (pt0) cc_final: 0.6035 (pt0) REVERT: H 108 LYS cc_start: 0.7308 (tttp) cc_final: 0.7021 (ttpp) outliers start: 0 outliers final: 1 residues processed: 146 average time/residue: 0.9263 time to fit residues: 142.6075 Evaluate side-chains 128 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN F 25 ASN F 27 GLN F 93 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.119943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.104254 restraints weight = 16292.838| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 0.83 r_work: 0.3215 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13166 Z= 0.157 Angle : 0.659 6.160 19112 Z= 0.389 Chirality : 0.048 0.210 2171 Planarity : 0.004 0.031 1347 Dihedral : 30.939 169.297 4225 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 1.12 % Allowed : 17.50 % Favored : 81.38 % 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: 2.56 (0.30), residues: 737 helix: 2.38 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.31 (0.39), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 71 TYR 0.018 0.001 TYR H 40 PHE 0.005 0.001 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.16 (13166) covalent geometry : angle 0.65879 / 0.39 (19112) hydrogen bonds : bond 0.05427 / 3.63 ( 810) hydrogen bonds : angle 3.01592 / 2.27 ( 2008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.304 Fit side-chains REVERT: A 83 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.6387 (mtm180) REVERT: A 106 ASP cc_start: 0.7593 (m-30) cc_final: 0.7369 (m-30) REVERT: D 71 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7339 (mt-10) REVERT: E 120 MET cc_start: 0.7999 (mtt) cc_final: 0.7786 (mtm) REVERT: F 84 MET cc_start: 0.8290 (mmm) cc_final: 0.7869 (tpp) REVERT: G 89 ASN cc_start: 0.8566 (m-40) cc_final: 0.8240 (m110) outliers start: 7 outliers final: 0 residues processed: 131 average time/residue: 0.9015 time to fit residues: 124.8107 Evaluate side-chains 123 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 121 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain D residue 71 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 93 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 68 GLN B 93 GLN D 84 ASN F 25 ASN F 27 GLN F 75 HIS G 73 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.113563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.097519 restraints weight = 16099.484| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 0.83 r_work: 0.3092 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13166 Z= 0.200 Angle : 0.692 6.181 19112 Z= 0.404 Chirality : 0.053 0.272 2171 Planarity : 0.005 0.040 1347 Dihedral : 30.827 170.995 4223 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.25 % Allowed : 18.62 % Favored : 79.13 % 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: 2.81 (0.30), residues: 737 helix: 2.59 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.27 (0.38), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 71 TYR 0.017 0.002 TYR F 98 PHE 0.007 0.002 PHE E 104 HIS 0.005 0.002 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.20 (13166) covalent geometry : angle 0.69236 / 0.40 (19112) hydrogen bonds : bond 0.06076 / 4.08 ( 810) hydrogen bonds : angle 2.96116 / 2.23 ( 2008) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.313 Fit side-chains REVERT: A 40 ARG cc_start: 0.8264 (mtp85) cc_final: 0.7945 (mtt-85) REVERT: A 63 ARG cc_start: 0.8395 (mmp80) cc_final: 0.8045 (mmt-90) REVERT: A 83 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.6547 (mtm180) REVERT: A 106 ASP cc_start: 0.7604 (m-30) cc_final: 0.7380 (m-30) REVERT: A 128 ARG cc_start: 0.8682 (mtp180) cc_final: 0.8309 (mmm160) REVERT: D 71 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7366 (mt-10) REVERT: E 120 MET cc_start: 0.8079 (mtt) cc_final: 0.7858 (mtm) REVERT: G 17 ARG cc_start: 0.8593 (mtm-85) cc_final: 0.8338 (mtm180) REVERT: G 42 ARG cc_start: 0.8202 (mtp85) cc_final: 0.7995 (mtt-85) REVERT: G 73 ASN cc_start: 0.7998 (t0) cc_final: 0.7620 (t160) REVERT: G 89 ASN cc_start: 0.8738 (m-40) cc_final: 0.8503 (m-40) outliers start: 14 outliers final: 2 residues processed: 115 average time/residue: 0.9639 time to fit residues: 116.6239 Evaluate side-chains 111 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 107 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 44 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 125 GLN B 93 GLN C 73 ASN F 25 ASN H 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.115303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.099381 restraints weight = 16085.560| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 0.83 r_work: 0.3137 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13166 Z= 0.150 Angle : 0.655 6.061 19112 Z= 0.381 Chirality : 0.049 0.257 2171 Planarity : 0.004 0.038 1347 Dihedral : 30.830 172.283 4223 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.44 % Allowed : 19.10 % Favored : 79.45 % 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: 2.96 (0.30), residues: 737 helix: 2.73 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.38 (0.38), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 71 TYR 0.011 0.001 TYR H 40 PHE 0.008 0.001 PHE D 70 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 (13166) covalent geometry : angle 0.65501 / 0.38 (19112) hydrogen bonds : bond 0.05243 / 3.53 ( 810) hydrogen bonds : angle 2.83765 / 2.14 ( 2008) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.305 Fit side-chains REVERT: A 63 ARG cc_start: 0.8336 (mmp80) cc_final: 0.7987 (mmt-90) REVERT: A 83 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.6532 (mtm180) REVERT: A 106 ASP cc_start: 0.7630 (m-30) cc_final: 0.7357 (m-30) REVERT: A 128 ARG cc_start: 0.8695 (mtp180) cc_final: 0.8360 (mmm160) REVERT: D 71 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7278 (mt-10) REVERT: G 73 ASN cc_start: 0.7997 (t0) cc_final: 0.7610 (t160) REVERT: G 89 ASN cc_start: 0.8697 (m-40) cc_final: 0.8367 (m110) REVERT: G 91 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.5296 (tp30) REVERT: H 79 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7801 (mtt90) REVERT: H 93 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7081 (mp0) outliers start: 9 outliers final: 1 residues processed: 116 average time/residue: 1.0245 time to fit residues: 124.7528 Evaluate side-chains 112 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 73 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 44 optimal weight: 0.0040 chunk 86 optimal weight: 9.9990 chunk 41 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS B 93 GLN F 25 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.116216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.100298 restraints weight = 16149.948| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 0.84 r_work: 0.3137 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13166 Z= 0.154 Angle : 0.625 5.806 19112 Z= 0.368 Chirality : 0.047 0.258 2171 Planarity : 0.004 0.039 1347 Dihedral : 30.827 173.032 4223 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.09 % Allowed : 19.42 % Favored : 78.49 % 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: 3.08 (0.30), residues: 737 helix: 2.80 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.27 (0.38), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 71 TYR 0.009 0.001 TYR D 40 PHE 0.007 0.001 PHE A 67 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (13166) covalent geometry : angle 0.62468 / 0.37 (19112) hydrogen bonds : bond 0.04938 / 3.32 ( 810) hydrogen bonds : angle 2.76756 / 2.09 ( 2008) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.289 Fit side-chains REVERT: A 63 ARG cc_start: 0.8320 (mmp80) cc_final: 0.8017 (mmt-90) REVERT: A 83 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.6585 (mtm180) REVERT: A 128 ARG cc_start: 0.8683 (mtp180) cc_final: 0.8316 (mmm160) REVERT: B 95 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7487 (mtt-85) REVERT: D 71 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: G 73 ASN cc_start: 0.8061 (t0) cc_final: 0.7608 (t160) REVERT: G 77 ARG cc_start: 0.8507 (mtm-85) cc_final: 0.8167 (mtm180) REVERT: G 91 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.5124 (tp30) REVERT: H 93 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7246 (mp0) outliers start: 13 outliers final: 4 residues processed: 112 average time/residue: 1.0210 time to fit residues: 119.9697 Evaluate side-chains 110 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 28 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN F 27 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.116496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.100632 restraints weight = 16026.097| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 0.83 r_work: 0.3154 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13166 Z= 0.146 Angle : 0.619 6.010 19112 Z= 0.365 Chirality : 0.046 0.256 2171 Planarity : 0.004 0.041 1347 Dihedral : 30.821 173.775 4223 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.12 % Allowed : 20.87 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.15 (0.30), residues: 737 helix: 2.85 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.24 (0.39), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 129 TYR 0.013 0.001 TYR F 88 PHE 0.006 0.001 PHE A 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.15 (13166) covalent geometry : angle 0.61944 / 0.36 (19112) hydrogen bonds : bond 0.04819 / 3.23 ( 810) hydrogen bonds : angle 2.73106 / 2.06 ( 2008) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.295 Fit side-chains REVERT: A 42 ARG cc_start: 0.7838 (mtt90) cc_final: 0.7610 (mtt90) REVERT: A 63 ARG cc_start: 0.8299 (mmp80) cc_final: 0.7984 (mmt-90) REVERT: A 83 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.6585 (mtm180) REVERT: A 128 ARG cc_start: 0.8675 (mtp180) cc_final: 0.8302 (mmm160) REVERT: B 95 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7458 (mtt-85) REVERT: D 71 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: G 73 ASN cc_start: 0.8076 (t0) cc_final: 0.7644 (t160) REVERT: G 77 ARG cc_start: 0.8498 (mtm-85) cc_final: 0.8166 (mtm180) REVERT: G 91 GLU cc_start: 0.6348 (OUTLIER) cc_final: 0.5114 (tp30) REVERT: H 79 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7813 (mtt90) REVERT: H 93 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7243 (mp0) outliers start: 7 outliers final: 1 residues processed: 102 average time/residue: 1.0938 time to fit residues: 116.7928 Evaluate side-chains 105 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 48 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN F 27 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.115020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.099137 restraints weight = 15854.323| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 0.82 r_work: 0.3117 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13166 Z= 0.169 Angle : 0.642 6.452 19112 Z= 0.374 Chirality : 0.048 0.254 2171 Planarity : 0.004 0.041 1347 Dihedral : 30.787 174.573 4223 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.77 % Allowed : 20.87 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.01 (0.30), residues: 737 helix: 2.75 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.29 (0.39), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 52 TYR 0.013 0.002 TYR D 40 PHE 0.006 0.001 PHE A 67 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.17 (13166) covalent geometry : angle 0.64200 / 0.37 (19112) hydrogen bonds : bond 0.05164 / 3.46 ( 810) hydrogen bonds : angle 2.75528 / 2.07 ( 2008) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.312 Fit side-chains REVERT: A 42 ARG cc_start: 0.7894 (mtt90) cc_final: 0.7654 (mtt90) REVERT: A 63 ARG cc_start: 0.8343 (mmp80) cc_final: 0.8002 (mmt-90) REVERT: A 83 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.6765 (mtm180) REVERT: B 95 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7366 (mtp-110) REVERT: D 71 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7050 (mp0) REVERT: G 73 ASN cc_start: 0.8139 (t0) cc_final: 0.7726 (t160) REVERT: G 77 ARG cc_start: 0.8515 (mtm-85) cc_final: 0.8185 (mtm180) REVERT: G 91 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.5111 (tp30) REVERT: H 93 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7239 (mp0) outliers start: 11 outliers final: 1 residues processed: 103 average time/residue: 1.1266 time to fit residues: 121.5046 Evaluate side-chains 105 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 52 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 70 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN E 68 GLN F 27 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.113707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.097784 restraints weight = 15971.697| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 0.82 r_work: 0.3097 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13166 Z= 0.191 Angle : 0.666 7.617 19112 Z= 0.384 Chirality : 0.050 0.267 2171 Planarity : 0.004 0.043 1347 Dihedral : 30.796 175.138 4223 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.44 % Allowed : 20.71 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.30), residues: 737 helix: 2.66 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.33 (0.38), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 40 TYR 0.013 0.002 TYR D 40 PHE 0.006 0.001 PHE H 70 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.19 (13166) covalent geometry : angle 0.66554 / 0.38 (19112) hydrogen bonds : bond 0.05441 / 3.66 ( 810) hydrogen bonds : angle 2.79413 / 2.10 ( 2008) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.302 Fit side-chains REVERT: A 42 ARG cc_start: 0.7930 (mtt90) cc_final: 0.7680 (mtt90) REVERT: A 63 ARG cc_start: 0.8364 (mmp80) cc_final: 0.7991 (mmt-90) REVERT: A 83 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.6822 (mtm180) REVERT: A 128 ARG cc_start: 0.8671 (mtp180) cc_final: 0.8289 (mmm160) REVERT: B 95 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7497 (mtt-85) REVERT: D 71 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: G 73 ASN cc_start: 0.8183 (t0) cc_final: 0.7742 (t0) REVERT: G 77 ARG cc_start: 0.8501 (mtm-85) cc_final: 0.8176 (mtm180) REVERT: G 91 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.5002 (tp30) REVERT: H 93 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7227 (mp0) outliers start: 9 outliers final: 2 residues processed: 104 average time/residue: 1.1112 time to fit residues: 120.9418 Evaluate side-chains 99 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 0.0670 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.114217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.098297 restraints weight = 15911.870| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 0.82 r_work: 0.3107 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13166 Z= 0.159 Angle : 0.658 7.519 19112 Z= 0.380 Chirality : 0.049 0.259 2171 Planarity : 0.004 0.051 1347 Dihedral : 30.799 175.250 4223 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.77 % Allowed : 20.39 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.95 (0.30), residues: 737 helix: 2.73 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.38 (0.38), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 129 TYR 0.012 0.001 TYR D 40 PHE 0.006 0.001 PHE A 67 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.16 (13166) covalent geometry : angle 0.65832 / 0.38 (19112) hydrogen bonds : bond 0.05216 / 3.50 ( 810) hydrogen bonds : angle 2.77971 / 2.09 ( 2008) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.296 Fit side-chains REVERT: A 42 ARG cc_start: 0.7937 (mtt90) cc_final: 0.7679 (mtt90) REVERT: A 63 ARG cc_start: 0.8351 (mmp80) cc_final: 0.8099 (mmt-90) REVERT: A 83 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.6849 (mtm180) REVERT: A 128 ARG cc_start: 0.8679 (mtp180) cc_final: 0.8301 (mmm160) REVERT: B 95 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7397 (mtp-110) REVERT: D 71 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: E 133 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6863 (mt-10) REVERT: G 73 ASN cc_start: 0.8174 (t0) cc_final: 0.7743 (t0) REVERT: G 91 GLU cc_start: 0.6403 (OUTLIER) cc_final: 0.4986 (tp30) REVERT: H 93 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7248 (mp0) outliers start: 11 outliers final: 4 residues processed: 99 average time/residue: 1.0515 time to fit residues: 109.0057 Evaluate side-chains 102 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 49 optimal weight: 0.0770 chunk 84 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN C 73 ASN F 27 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.114413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.098548 restraints weight = 16070.400| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 0.82 r_work: 0.3113 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13166 Z= 0.174 Angle : 0.650 6.433 19112 Z= 0.377 Chirality : 0.049 0.258 2171 Planarity : 0.004 0.043 1347 Dihedral : 30.816 175.453 4223 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.77 % Allowed : 20.22 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.94 (0.30), residues: 737 helix: 2.71 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.30 (0.38), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 129 TYR 0.012 0.001 TYR D 40 PHE 0.006 0.001 PHE A 67 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (13166) covalent geometry : angle 0.64994 / 0.38 (19112) hydrogen bonds : bond 0.05177 / 3.48 ( 810) hydrogen bonds : angle 2.76662 / 2.08 ( 2008) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.289 Fit side-chains REVERT: A 42 ARG cc_start: 0.7927 (mtt90) cc_final: 0.7664 (mtt90) REVERT: A 63 ARG cc_start: 0.8347 (mmp80) cc_final: 0.8020 (mmt-90) REVERT: A 83 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.6836 (mtm180) REVERT: A 128 ARG cc_start: 0.8661 (mtp180) cc_final: 0.8323 (mmm160) REVERT: A 131 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8252 (mtt-85) REVERT: B 95 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7389 (mtp-110) REVERT: D 71 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: E 133 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6899 (mt-10) REVERT: G 73 ASN cc_start: 0.8208 (t0) cc_final: 0.7774 (t0) REVERT: G 91 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.4970 (tp30) REVERT: H 59 MET cc_start: 0.8743 (tpt) cc_final: 0.8043 (tpt) REVERT: H 93 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7238 (mp0) outliers start: 11 outliers final: 2 residues processed: 99 average time/residue: 1.0583 time to fit residues: 109.6511 Evaluate side-chains 101 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 9 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 37 optimal weight: 0.0970 chunk 88 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN F 27 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.114731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.098941 restraints weight = 15916.110| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 0.81 r_work: 0.3127 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13166 Z= 0.146 Angle : 0.643 6.555 19112 Z= 0.374 Chirality : 0.048 0.255 2171 Planarity : 0.004 0.042 1347 Dihedral : 30.820 175.478 4223 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.61 % Allowed : 20.22 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.00 (0.30), residues: 737 helix: 2.75 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.28 (0.38), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 129 TYR 0.011 0.001 TYR D 40 PHE 0.006 0.001 PHE A 67 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.15 (13166) covalent geometry : angle 0.64342 / 0.37 (19112) hydrogen bonds : bond 0.05070 / 3.41 ( 810) hydrogen bonds : angle 2.76050 / 2.07 ( 2008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3940.42 seconds wall clock time: 67 minutes 41.15 seconds (4061.15 seconds total)