Starting phenix.real_space_refine on Tue Aug 4 17:35:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w5m_37297/08_2026/8w5m_37297.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w5m_37297/08_2026/8w5m_37297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w5m_37297/08_2026/8w5m_37297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w5m_37297/08_2026/8w5m_37297.map" model { file = "/net/cci-nas-00/data/ceres_data/8w5m_37297/08_2026/8w5m_37297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w5m_37297/08_2026/8w5m_37297.cif" } resolution = 3.1 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= 0.005 sd= 0.078 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: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 3519 2.51 5 N 995 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5645 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 777 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "H" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 924 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "A" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 980 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "b" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 992 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain: "B" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 992 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain: "C" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 980 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Time building chain proxies: 1.53, per 1000 atoms: 0.27 Number of scatterers: 5645 At special positions: 0 Unit cell: (101.64, 109.56, 89.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 1116 8.00 N 995 7.00 C 3519 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS L 25 " - pdb=" SG CYS L 93 " distance=2.03 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: 0.32 Conformation dependent library (CDL) restraints added in 258.6 milliseconds 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1388 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 9 sheets defined 12.8% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 101 through 116 removed outlier: 3.583A pdb=" N ARG A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 125 Processing helix chain 'b' and resid 101 through 116 removed outlier: 3.583A pdb=" N ARG b 105 " --> pdb=" O THR b 101 " (cutoff:3.500A) Processing helix chain 'b' and resid 118 through 125 Processing helix chain 'B' and resid 101 through 116 removed outlier: 3.584A pdb=" N ARG B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'C' and resid 101 through 116 removed outlier: 3.584A pdb=" N ARG C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 125 Processing sheet with id=AA1, first strand: chain 'L' and resid 8 through 9 Processing sheet with id=AA2, first strand: chain 'L' and resid 21 through 22 Processing sheet with id=AA3, first strand: chain 'L' and resid 48 through 53 removed outlier: 6.584A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 94 through 96 Processing sheet with id=AA5, first strand: chain 'H' and resid 7 through 10 removed outlier: 3.842A pdb=" N LEU H 7 " --> pdb=" O ALA H 26 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU H 9 " --> pdb=" O SER H 24 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER H 24 " --> pdb=" O GLU H 9 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER H 74 " --> pdb=" O PHE H 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 50 through 54 removed outlier: 6.874A pdb=" N TRP H 39 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N TYR H 53 " --> pdb=" O MET H 37 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG H 42 " --> pdb=" O MET H 96 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET H 96 " --> pdb=" O ARG H 42 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA H 95 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR H 117 " --> pdb=" O TYR H 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 6 through 11 removed outlier: 5.243A pdb=" N THR A 7 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU A 21 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY A 9 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU A 19 " --> pdb=" O GLY A 9 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER A 34 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL A 26 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL A 32 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG A 86 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N CYS A 74 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL A 84 " --> pdb=" O CYS A 74 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER b 95 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL b 84 " --> pdb=" O CYS b 74 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N CYS b 74 " --> pdb=" O VAL b 84 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG b 86 " --> pdb=" O THR b 72 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL b 32 " --> pdb=" O VAL b 26 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL b 26 " --> pdb=" O VAL b 32 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N SER b 34 " --> pdb=" O ARG b 24 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU b 19 " --> pdb=" O GLY b 9 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY b 9 " --> pdb=" O LEU b 19 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU b 21 " --> pdb=" O THR b 7 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N THR b 7 " --> pdb=" O LEU b 21 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 6 through 11 removed outlier: 5.243A pdb=" N THR B 7 " --> pdb=" O LEU B 21 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU B 21 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY B 9 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 19 " --> pdb=" O GLY B 9 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N SER B 34 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL B 26 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL B 32 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG B 86 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N CYS B 74 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL B 84 " --> pdb=" O CYS B 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 6 through 11 removed outlier: 5.244A pdb=" N THR C 7 " --> pdb=" O LEU C 21 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU C 21 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY C 9 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU C 19 " --> pdb=" O GLY C 9 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER C 34 " --> pdb=" O ARG C 24 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL C 26 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG C 86 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N CYS C 74 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL C 84 " --> pdb=" O CYS C 74 " (cutoff:3.500A) 211 hydrogen bonds defined for protein. 582 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.78 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 958 1.29 - 1.42: 1378 1.42 - 1.55: 3372 1.55 - 1.68: 14 1.68 - 1.81: 18 Bond restraints: 5740 Sorted by residual: bond pdb=" C VAL A 6 " pdb=" O VAL A 6 " ideal model delta sigma weight residual 1.236 1.156 0.081 1.20e-02 6.94e+03 4.53e+01 bond pdb=" C LEU A 3 " pdb=" O LEU A 3 " ideal model delta sigma weight residual 1.235 1.169 0.066 1.20e-02 6.94e+03 2.99e+01 bond pdb=" C THR A 5 " pdb=" O THR A 5 " ideal model delta sigma weight residual 1.234 1.171 0.063 1.20e-02 6.94e+03 2.76e+01 bond pdb=" CB THR A 5 " pdb=" CG2 THR A 5 " ideal model delta sigma weight residual 1.521 1.377 0.144 3.30e-02 9.18e+02 1.90e+01 bond pdb=" CA THR A 5 " pdb=" CB THR A 5 " ideal model delta sigma weight residual 1.529 1.461 0.068 1.64e-02 3.72e+03 1.70e+01 ... (remaining 5735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 7509 2.20 - 4.39: 249 4.39 - 6.59: 35 6.59 - 8.79: 13 8.79 - 10.98: 7 Bond angle restraints: 7813 Sorted by residual: angle pdb=" C SER C 53 " pdb=" N GLN C 54 " pdb=" CA GLN C 54 " ideal model delta sigma weight residual 120.86 130.18 -9.32 1.60e+00 3.91e-01 3.39e+01 angle pdb=" C SER b 53 " pdb=" N GLN b 54 " pdb=" CA GLN b 54 " ideal model delta sigma weight residual 120.86 130.16 -9.30 1.60e+00 3.91e-01 3.38e+01 angle pdb=" C SER B 53 " pdb=" N GLN B 54 " pdb=" CA GLN B 54 " ideal model delta sigma weight residual 120.86 130.15 -9.29 1.60e+00 3.91e-01 3.37e+01 angle pdb=" C SER A 53 " pdb=" N GLN A 54 " pdb=" CA GLN A 54 " ideal model delta sigma weight residual 120.86 130.13 -9.27 1.60e+00 3.91e-01 3.36e+01 angle pdb=" N VAL A 6 " pdb=" CA VAL A 6 " pdb=" CB VAL A 6 " ideal model delta sigma weight residual 111.83 105.69 6.14 1.23e+00 6.61e-01 2.49e+01 ... (remaining 7808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.03: 3316 14.03 - 28.06: 123 28.06 - 42.09: 29 42.09 - 56.12: 0 56.12 - 70.15: 4 Dihedral angle restraints: 3472 sinusoidal: 1315 harmonic: 2157 Sorted by residual: dihedral pdb=" CA GLY L 18 " pdb=" C GLY L 18 " pdb=" N GLU L 19 " pdb=" CA GLU L 19 " ideal model delta harmonic sigma weight residual 180.00 141.49 38.51 0 5.00e+00 4.00e-02 5.93e+01 dihedral pdb=" CA ASP H 65 " pdb=" C ASP H 65 " pdb=" N THR H 66 " pdb=" CA THR H 66 " ideal model delta harmonic sigma weight residual 180.00 151.56 28.44 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA CYS H 99 " pdb=" C CYS H 99 " pdb=" N ALA H 100 " pdb=" CA ALA H 100 " ideal model delta harmonic sigma weight residual -180.00 -151.88 -28.12 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 3469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 599 0.050 - 0.101: 217 0.101 - 0.151: 74 0.151 - 0.201: 20 0.201 - 0.251: 11 Chirality restraints: 921 Sorted by residual: chirality pdb=" CA VAL A 6 " pdb=" N VAL A 6 " pdb=" C VAL A 6 " pdb=" CB VAL A 6 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CG LEU b 128 " pdb=" CB LEU b 128 " pdb=" CD1 LEU b 128 " pdb=" CD2 LEU b 128 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CG LEU C 128 " pdb=" CB LEU C 128 " pdb=" CD1 LEU C 128 " pdb=" CD2 LEU C 128 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 918 not shown) Planarity restraints: 1021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY L 18 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.09e+00 pdb=" C GLY L 18 " 0.046 2.00e-02 2.50e+03 pdb=" O GLY L 18 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU L 19 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 67 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" C VAL H 67 " 0.043 2.00e-02 2.50e+03 pdb=" O VAL H 67 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS H 68 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL b 41 " 0.040 5.00e-02 4.00e+02 6.13e-02 6.01e+00 pdb=" N PRO b 42 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO b 42 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO b 42 " 0.033 5.00e-02 4.00e+02 ... (remaining 1018 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1364 2.80 - 3.32: 4481 3.32 - 3.85: 8661 3.85 - 4.37: 9553 4.37 - 4.90: 17345 Nonbonded interactions: 41404 Sorted by model distance: nonbonded pdb=" N ALA A 1 " pdb=" OD2 ASP b 123 " model vdw 2.272 3.120 nonbonded pdb=" OG1 THR H 72 " pdb=" O GLN H 85 " model vdw 2.329 3.040 nonbonded pdb=" O ASP H 105 " pdb=" OH TYR H 109 " model vdw 2.369 3.040 nonbonded pdb=" OE1 GLN B 87 " pdb=" OH TYR B 89 " model vdw 2.402 3.040 nonbonded pdb=" OE1 GLN A 87 " pdb=" OH TYR A 89 " model vdw 2.402 3.040 ... (remaining 41399 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' selection = (chain 'B' and resid 1 through 131) selection = chain 'C' selection = (chain 'b' and resid 1 through 131) } 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.030 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 : 0.006 0.144 5741 Z= 0.309 Angle : 0.981 10.984 7815 Z= 0.546 Chirality : 0.063 0.251 921 Planarity : 0.008 0.061 1021 Dihedral : 8.719 70.155 2081 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.16 % Allowed : 4.38 % Favored : 95.45 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.59 (0.26), residues: 739 helix: -2.05 (0.44), residues: 92 sheet: -1.48 (0.29), residues: 301 loop : -3.34 (0.22), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG H 102 TYR 0.021 0.003 TYR b 62 PHE 0.024 0.003 PHE H 71 TRP 0.028 0.002 TRP H 113 HIS 0.008 0.003 HIS H 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.31 ( 5740) covalent geometry : angle 0.98160 / 0.55 ( 7813) SS BOND : bond 0.00060 / 0.03 ( 1) SS BOND : angle 0.41650 / 0.28 ( 2) hydrogen bonds : bond 0.14308 / 9.24 ( 211) hydrogen bonds : angle 6.66526 / 4.61 ( 582) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.215 Fit side-chains REVERT: L 72 ILE cc_start: 0.9129 (mt) cc_final: 0.8779 (pt) REVERT: L 102 VAL cc_start: 0.8596 (t) cc_final: 0.8395 (m) REVERT: H 21 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7021 (tm) REVERT: H 74 SER cc_start: 0.8886 (t) cc_final: 0.8254 (p) REVERT: A 53 SER cc_start: 0.8085 (m) cc_final: 0.7660 (t) REVERT: b 2 LYS cc_start: 0.7997 (tttt) cc_final: 0.7516 (mmtt) REVERT: b 24 ARG cc_start: 0.8211 (mtp180) cc_final: 0.6545 (tpt170) REVERT: b 53 SER cc_start: 0.8613 (m) cc_final: 0.8399 (t) REVERT: b 60 LYS cc_start: 0.8426 (pttm) cc_final: 0.8221 (ptpp) REVERT: b 102 ASP cc_start: 0.8366 (p0) cc_final: 0.8134 (p0) REVERT: C 34 SER cc_start: 0.8797 (m) cc_final: 0.8546 (t) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.0919 time to fit residues: 18.8331 Evaluate side-chains 111 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.0040 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 36 ASN L 57 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN b 61 ASN b 77 ASN B 61 ASN C 61 ASN C 70 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.136661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.103732 restraints weight = 7348.629| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.74 r_work: 0.3119 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5741 Z= 0.169 Angle : 0.626 7.812 7815 Z= 0.331 Chirality : 0.048 0.145 921 Planarity : 0.006 0.050 1021 Dihedral : 5.219 38.536 808 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.60 % Allowed : 9.58 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.28), residues: 739 helix: -0.51 (0.53), residues: 94 sheet: -0.98 (0.28), residues: 323 loop : -3.06 (0.25), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 57 TYR 0.015 0.002 TYR H 63 PHE 0.018 0.002 PHE H 71 TRP 0.017 0.002 TRP H 113 HIS 0.007 0.002 HIS H 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 5740) covalent geometry : angle 0.62566 / 0.33 ( 7813) SS BOND : bond 0.00043 / 0.02 ( 1) SS BOND : angle 0.79454 / 0.53 ( 2) hydrogen bonds : bond 0.04264 / 2.94 ( 211) hydrogen bonds : angle 5.25992 / 3.53 ( 582) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: L 23 LEU cc_start: 0.8558 (mp) cc_final: 0.8283 (mp) REVERT: L 72 ILE cc_start: 0.9163 (mt) cc_final: 0.8783 (pt) REVERT: H 25 CYS cc_start: 0.8073 (p) cc_final: 0.7676 (t) REVERT: b 2 LYS cc_start: 0.8338 (tttt) cc_final: 0.7602 (mmtt) REVERT: b 24 ARG cc_start: 0.8891 (mtp180) cc_final: 0.6406 (tpt170) REVERT: b 60 LYS cc_start: 0.8967 (pttm) cc_final: 0.8525 (ptpp) REVERT: b 123 ASP cc_start: 0.9160 (t70) cc_final: 0.8752 (t0) REVERT: b 127 GLN cc_start: 0.9058 (mp10) cc_final: 0.8852 (mm110) REVERT: B 47 ARG cc_start: 0.8464 (ptp-170) cc_final: 0.8095 (ptp-110) REVERT: C 16 LYS cc_start: 0.9213 (mttt) cc_final: 0.8889 (mttt) REVERT: C 121 LEU cc_start: 0.8687 (mm) cc_final: 0.8414 (mt) outliers start: 16 outliers final: 8 residues processed: 136 average time/residue: 0.1068 time to fit residues: 17.9189 Evaluate side-chains 110 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain C residue 51 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 2 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 33 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.6489 > 50:) chunk 25 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 22 ASN ** b 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 87 GLN B 22 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.127571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.095226 restraints weight = 7521.060| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.68 r_work: 0.3011 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 5741 Z= 0.335 Angle : 0.733 6.707 7815 Z= 0.393 Chirality : 0.055 0.169 921 Planarity : 0.006 0.051 1021 Dihedral : 5.614 38.668 808 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 5.19 % Allowed : 11.20 % Favored : 83.60 % 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: -2.58 (0.28), residues: 739 helix: -0.80 (0.53), residues: 94 sheet: -0.92 (0.28), residues: 327 loop : -2.85 (0.26), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 57 TYR 0.029 0.003 TYR b 62 PHE 0.018 0.002 PHE H 71 TRP 0.013 0.002 TRP H 113 HIS 0.024 0.006 HIS L 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00807 / 0.34 ( 5740) covalent geometry : angle 0.73249 / 0.39 ( 7813) SS BOND : bond 0.00466 / 0.25 ( 1) SS BOND : angle 2.26039 / 1.51 ( 2) hydrogen bonds : bond 0.05185 / 3.57 ( 211) hydrogen bonds : angle 5.42316 / 3.64 ( 582) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8868 (t70) cc_final: 0.8411 (t0) REVERT: b 2 LYS cc_start: 0.8554 (tttt) cc_final: 0.7870 (mmtt) REVERT: b 24 ARG cc_start: 0.9212 (mtp180) cc_final: 0.7064 (tpt170) REVERT: b 60 LYS cc_start: 0.8995 (pttm) cc_final: 0.8666 (ptpp) REVERT: b 123 ASP cc_start: 0.9190 (t70) cc_final: 0.8819 (t0) REVERT: B 47 ARG cc_start: 0.8630 (ptp-170) cc_final: 0.8415 (ptp90) REVERT: B 61 ASN cc_start: 0.8573 (m-40) cc_final: 0.8328 (m-40) REVERT: C 2 LYS cc_start: 0.8536 (tttt) cc_final: 0.6462 (mmtt) REVERT: C 45 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8126 (mm-30) REVERT: C 87 GLN cc_start: 0.9181 (mt0) cc_final: 0.8930 (mt0) REVERT: C 121 LEU cc_start: 0.8919 (mm) cc_final: 0.8661 (mt) REVERT: C 122 ILE cc_start: 0.8731 (pt) cc_final: 0.8167 (mm) outliers start: 32 outliers final: 21 residues processed: 135 average time/residue: 0.0991 time to fit residues: 17.0743 Evaluate side-chains 126 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain b residue 122 ILE Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 93 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN C 22 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.131332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.099516 restraints weight = 7413.659| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.66 r_work: 0.3047 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5741 Z= 0.149 Angle : 0.578 5.868 7815 Z= 0.309 Chirality : 0.048 0.155 921 Planarity : 0.005 0.044 1021 Dihedral : 4.860 31.432 808 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.22 % Allowed : 12.99 % Favored : 82.79 % 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: -2.17 (0.28), residues: 739 helix: -0.20 (0.55), residues: 94 sheet: -0.60 (0.28), residues: 320 loop : -2.71 (0.27), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 90 TYR 0.015 0.002 TYR b 62 PHE 0.007 0.001 PHE H 71 TRP 0.012 0.001 TRP H 113 HIS 0.026 0.005 HIS L 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 5740) covalent geometry : angle 0.57822 / 0.31 ( 7813) SS BOND : bond 0.00162 / 0.09 ( 1) SS BOND : angle 0.95820 / 0.64 ( 2) hydrogen bonds : bond 0.04037 / 2.80 ( 211) hydrogen bonds : angle 4.97112 / 3.33 ( 582) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: H 21 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.6967 (tm) REVERT: H 105 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7307 (t0) REVERT: A 45 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8193 (tt0) REVERT: b 2 LYS cc_start: 0.8532 (tttt) cc_final: 0.7840 (mmtt) REVERT: b 24 ARG cc_start: 0.9047 (mtp180) cc_final: 0.6403 (tpt170) REVERT: b 60 LYS cc_start: 0.8949 (pttm) cc_final: 0.8623 (ptpp) REVERT: b 123 ASP cc_start: 0.9190 (t70) cc_final: 0.8915 (t0) REVERT: B 47 ARG cc_start: 0.8558 (ptp-170) cc_final: 0.8137 (ptp-110) REVERT: B 61 ASN cc_start: 0.8552 (m-40) cc_final: 0.8220 (m-40) REVERT: C 2 LYS cc_start: 0.8501 (tttt) cc_final: 0.6480 (mmtt) REVERT: C 45 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8039 (mm-30) REVERT: C 87 GLN cc_start: 0.9261 (mt0) cc_final: 0.8993 (mt0) REVERT: C 121 LEU cc_start: 0.8775 (mm) cc_final: 0.8462 (mt) REVERT: C 122 ILE cc_start: 0.8635 (pt) cc_final: 0.8162 (mm) outliers start: 26 outliers final: 17 residues processed: 123 average time/residue: 0.1007 time to fit residues: 15.6908 Evaluate side-chains 117 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 85 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN B 10 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.129065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.097146 restraints weight = 7610.523| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.70 r_work: 0.3023 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5741 Z= 0.220 Angle : 0.630 6.718 7815 Z= 0.335 Chirality : 0.051 0.187 921 Planarity : 0.005 0.046 1021 Dihedral : 5.006 34.342 808 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.55 % Allowed : 13.31 % Favored : 82.14 % 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: -2.23 (0.28), residues: 739 helix: -0.35 (0.54), residues: 96 sheet: -0.66 (0.29), residues: 324 loop : -2.74 (0.26), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 90 TYR 0.021 0.002 TYR b 62 PHE 0.011 0.002 PHE H 71 TRP 0.008 0.001 TRP H 113 HIS 0.006 0.003 HIS L 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 ( 5740) covalent geometry : angle 0.62940 / 0.33 ( 7813) SS BOND : bond 0.00307 / 0.16 ( 1) SS BOND : angle 1.44406 / 0.96 ( 2) hydrogen bonds : bond 0.04441 / 3.08 ( 211) hydrogen bonds : angle 5.04245 / 3.39 ( 582) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: L 109 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8002 (tp) REVERT: H 96 MET cc_start: 0.6510 (mtm) cc_final: 0.6302 (ttm) REVERT: H 105 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7417 (t0) REVERT: A 45 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8318 (tt0) REVERT: b 2 LYS cc_start: 0.8601 (tttt) cc_final: 0.7869 (mmtt) REVERT: b 24 ARG cc_start: 0.9150 (mtp180) cc_final: 0.7177 (tpt170) REVERT: b 60 LYS cc_start: 0.8975 (pttm) cc_final: 0.8670 (ptpp) REVERT: b 123 ASP cc_start: 0.9206 (t70) cc_final: 0.8939 (t0) REVERT: B 47 ARG cc_start: 0.8594 (ptp-170) cc_final: 0.8186 (ptp-110) REVERT: B 61 ASN cc_start: 0.8635 (m-40) cc_final: 0.8351 (m-40) REVERT: C 2 LYS cc_start: 0.8553 (tttt) cc_final: 0.6439 (mmtt) REVERT: C 45 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8013 (mm-30) REVERT: C 121 LEU cc_start: 0.8862 (mm) cc_final: 0.8576 (mt) REVERT: C 122 ILE cc_start: 0.8690 (pt) cc_final: 0.8213 (mm) outliers start: 28 outliers final: 22 residues processed: 125 average time/residue: 0.0914 time to fit residues: 14.5416 Evaluate side-chains 128 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 85 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 51 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN C 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.130907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.099276 restraints weight = 7483.342| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.67 r_work: 0.3056 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5741 Z= 0.144 Angle : 0.571 6.880 7815 Z= 0.304 Chirality : 0.048 0.184 921 Planarity : 0.004 0.043 1021 Dihedral : 4.650 30.481 808 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 5.03 % Allowed : 13.96 % Favored : 81.01 % 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: -1.91 (0.29), residues: 739 helix: 0.01 (0.55), residues: 96 sheet: -0.37 (0.29), residues: 312 loop : -2.60 (0.26), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 26 TYR 0.012 0.001 TYR b 62 PHE 0.021 0.001 PHE H 71 TRP 0.009 0.001 TRP H 113 HIS 0.006 0.002 HIS L 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 5740) covalent geometry : angle 0.57099 / 0.30 ( 7813) SS BOND : bond 0.00157 / 0.08 ( 1) SS BOND : angle 0.93466 / 0.62 ( 2) hydrogen bonds : bond 0.03939 / 2.74 ( 211) hydrogen bonds : angle 4.79053 / 3.22 ( 582) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: L 72 ILE cc_start: 0.9182 (mt) cc_final: 0.8854 (pt) REVERT: L 109 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.8009 (tp) REVERT: H 21 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.6732 (tm) REVERT: H 105 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7270 (t0) REVERT: b 2 LYS cc_start: 0.8585 (tttt) cc_final: 0.7892 (mmtt) REVERT: b 24 ARG cc_start: 0.9028 (mtp180) cc_final: 0.6886 (tpt170) REVERT: b 60 LYS cc_start: 0.8961 (pttm) cc_final: 0.8641 (ptpp) REVERT: b 123 ASP cc_start: 0.9192 (t70) cc_final: 0.8914 (t0) REVERT: B 47 ARG cc_start: 0.8583 (ptp-170) cc_final: 0.8202 (ptp-110) REVERT: B 61 ASN cc_start: 0.8595 (m-40) cc_final: 0.8257 (m-40) REVERT: C 2 LYS cc_start: 0.8541 (tttt) cc_final: 0.6445 (mmtt) REVERT: C 45 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8007 (mm-30) REVERT: C 121 LEU cc_start: 0.8797 (mm) cc_final: 0.8493 (mt) REVERT: C 122 ILE cc_start: 0.8700 (pt) cc_final: 0.8134 (mm) outliers start: 31 outliers final: 19 residues processed: 124 average time/residue: 0.0901 time to fit residues: 14.4352 Evaluate side-chains 121 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 85 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 41 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 47 HIS ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.126105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.094549 restraints weight = 7652.633| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.65 r_work: 0.2981 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 5741 Z= 0.332 Angle : 0.715 6.338 7815 Z= 0.379 Chirality : 0.055 0.183 921 Planarity : 0.005 0.046 1021 Dihedral : 5.286 36.992 808 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 5.68 % Allowed : 13.31 % Favored : 81.01 % 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: -2.26 (0.28), residues: 739 helix: -0.58 (0.53), residues: 96 sheet: -0.71 (0.28), residues: 334 loop : -2.69 (0.27), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG b 109 TYR 0.021 0.003 TYR C 62 PHE 0.031 0.002 PHE H 71 TRP 0.008 0.002 TRP L 96 HIS 0.007 0.003 HIS L 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00797 / 0.33 ( 5740) covalent geometry : angle 0.71446 / 0.38 ( 7813) SS BOND : bond 0.00427 / 0.22 ( 1) SS BOND : angle 1.99769 / 1.33 ( 2) hydrogen bonds : bond 0.04852 / 3.35 ( 211) hydrogen bonds : angle 5.16912 / 3.50 ( 582) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 0.215 Fit side-chains REVERT: L 109 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8119 (tp) REVERT: H 105 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7630 (t0) REVERT: A 45 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8220 (tt0) REVERT: A 81 ASP cc_start: 0.8233 (m-30) cc_final: 0.7238 (p0) REVERT: b 2 LYS cc_start: 0.8689 (tttt) cc_final: 0.7975 (mmtt) REVERT: b 24 ARG cc_start: 0.9215 (mtp180) cc_final: 0.7270 (tpt170) REVERT: b 60 LYS cc_start: 0.8973 (pttm) cc_final: 0.8696 (ptpp) REVERT: b 102 ASP cc_start: 0.8856 (p0) cc_final: 0.8652 (p0) REVERT: b 123 ASP cc_start: 0.9210 (t70) cc_final: 0.8819 (t0) REVERT: B 61 ASN cc_start: 0.8654 (m-40) cc_final: 0.8404 (m-40) REVERT: C 2 LYS cc_start: 0.8486 (tttt) cc_final: 0.6342 (mmtt) REVERT: C 45 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8289 (mm-30) REVERT: C 61 ASN cc_start: 0.8147 (m-40) cc_final: 0.7914 (m110) REVERT: C 121 LEU cc_start: 0.8940 (mm) cc_final: 0.8677 (mt) REVERT: C 122 ILE cc_start: 0.8783 (pt) cc_final: 0.8090 (mm) outliers start: 35 outliers final: 30 residues processed: 133 average time/residue: 0.0932 time to fit residues: 15.8305 Evaluate side-chains 138 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 47 HIS Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain b residue 122 ILE Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 85 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 17 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 47 HIS ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.123226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.092930 restraints weight = 7507.084| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.52 r_work: 0.2953 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5741 Z= 0.170 Angle : 0.591 6.674 7815 Z= 0.315 Chirality : 0.049 0.199 921 Planarity : 0.005 0.045 1021 Dihedral : 4.815 31.265 808 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.71 % Allowed : 14.94 % Favored : 80.36 % 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: -2.08 (0.28), residues: 739 helix: -0.12 (0.54), residues: 96 sheet: -0.60 (0.28), residues: 326 loop : -2.65 (0.26), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 26 TYR 0.012 0.002 TYR b 62 PHE 0.008 0.001 PHE H 98 TRP 0.008 0.001 TRP H 113 HIS 0.010 0.003 HIS L 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 5740) covalent geometry : angle 0.59072 / 0.31 ( 7813) SS BOND : bond 0.00202 / 0.11 ( 1) SS BOND : angle 1.12952 / 0.75 ( 2) hydrogen bonds : bond 0.04128 / 2.88 ( 211) hydrogen bonds : angle 4.84822 / 3.29 ( 582) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.201 Fit side-chains REVERT: L 109 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7989 (tp) REVERT: H 21 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6515 (tm) REVERT: H 105 ASP cc_start: 0.7699 (OUTLIER) cc_final: 0.7336 (t0) REVERT: A 81 ASP cc_start: 0.8187 (m-30) cc_final: 0.7203 (p0) REVERT: b 24 ARG cc_start: 0.9164 (mtp180) cc_final: 0.7144 (tpt170) REVERT: b 60 LYS cc_start: 0.8954 (pttm) cc_final: 0.8662 (ptpp) REVERT: b 102 ASP cc_start: 0.8825 (p0) cc_final: 0.8611 (p0) REVERT: b 123 ASP cc_start: 0.9208 (t70) cc_final: 0.8920 (t0) REVERT: B 47 ARG cc_start: 0.8452 (ptp90) cc_final: 0.8128 (ptp-110) REVERT: B 61 ASN cc_start: 0.8647 (m-40) cc_final: 0.8293 (m-40) REVERT: C 2 LYS cc_start: 0.8419 (tttt) cc_final: 0.6257 (mmtt) REVERT: C 45 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8236 (mm-30) REVERT: C 61 ASN cc_start: 0.8129 (m-40) cc_final: 0.7904 (m110) REVERT: C 121 LEU cc_start: 0.8772 (mm) cc_final: 0.8479 (mt) REVERT: C 122 ILE cc_start: 0.8560 (pt) cc_final: 0.8033 (mm) outliers start: 29 outliers final: 24 residues processed: 124 average time/residue: 0.0799 time to fit residues: 12.8865 Evaluate side-chains 129 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 47 HIS Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 85 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 18 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 47 HIS ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.122608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.092332 restraints weight = 7519.141| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.52 r_work: 0.2944 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5741 Z= 0.188 Angle : 0.601 7.173 7815 Z= 0.320 Chirality : 0.050 0.194 921 Planarity : 0.005 0.047 1021 Dihedral : 4.773 31.647 808 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 5.36 % Allowed : 14.77 % Favored : 79.87 % 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: -2.05 (0.28), residues: 739 helix: -0.04 (0.54), residues: 96 sheet: -0.57 (0.28), residues: 324 loop : -2.64 (0.26), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 26 TYR 0.013 0.002 TYR b 62 PHE 0.009 0.001 PHE H 98 TRP 0.008 0.001 TRP H 50 HIS 0.007 0.003 HIS L 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 ( 5740) covalent geometry : angle 0.60052 / 0.32 ( 7813) SS BOND : bond 0.00225 / 0.12 ( 1) SS BOND : angle 1.20734 / 0.80 ( 2) hydrogen bonds : bond 0.04171 / 2.90 ( 211) hydrogen bonds : angle 4.82657 / 3.27 ( 582) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.211 Fit side-chains REVERT: L 72 ILE cc_start: 0.9052 (mt) cc_final: 0.8590 (pt) REVERT: L 109 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8022 (tp) REVERT: H 105 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7486 (t0) REVERT: A 81 ASP cc_start: 0.8218 (m-30) cc_final: 0.7237 (p0) REVERT: b 24 ARG cc_start: 0.9077 (mtp180) cc_final: 0.6875 (tpt170) REVERT: b 60 LYS cc_start: 0.8965 (pttm) cc_final: 0.8670 (ptpp) REVERT: b 102 ASP cc_start: 0.8829 (p0) cc_final: 0.8613 (p0) REVERT: b 123 ASP cc_start: 0.9214 (t70) cc_final: 0.8925 (t0) REVERT: B 47 ARG cc_start: 0.8466 (ptp90) cc_final: 0.8071 (ptp-110) REVERT: B 61 ASN cc_start: 0.8669 (m-40) cc_final: 0.8332 (m-40) REVERT: C 2 LYS cc_start: 0.8412 (tttt) cc_final: 0.6238 (mmtt) REVERT: C 45 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8267 (mm-30) REVERT: C 61 ASN cc_start: 0.8179 (m-40) cc_final: 0.7954 (m110) REVERT: C 121 LEU cc_start: 0.8771 (mm) cc_final: 0.8479 (mt) REVERT: C 122 ILE cc_start: 0.8646 (pt) cc_final: 0.8070 (mm) outliers start: 33 outliers final: 28 residues processed: 126 average time/residue: 0.0894 time to fit residues: 14.3644 Evaluate side-chains 132 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 47 HIS Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 47 HIS ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.125105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.094912 restraints weight = 7584.145| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.54 r_work: 0.2979 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5741 Z= 0.120 Angle : 0.556 7.500 7815 Z= 0.296 Chirality : 0.047 0.214 921 Planarity : 0.004 0.046 1021 Dihedral : 4.487 28.585 808 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.22 % Allowed : 15.91 % Favored : 79.87 % 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: -1.78 (0.29), residues: 739 helix: 0.30 (0.56), residues: 96 sheet: -0.32 (0.29), residues: 312 loop : -2.55 (0.27), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 26 TYR 0.010 0.001 TYR H 63 PHE 0.007 0.001 PHE L 49 TRP 0.009 0.001 TRP H 113 HIS 0.006 0.002 HIS L 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 5740) covalent geometry : angle 0.55643 / 0.30 ( 7813) SS BOND : bond 0.00092 / 0.05 ( 1) SS BOND : angle 0.72856 / 0.49 ( 2) hydrogen bonds : bond 0.03759 / 2.63 ( 211) hydrogen bonds : angle 4.65093 / 3.15 ( 582) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.225 Fit side-chains REVERT: L 72 ILE cc_start: 0.9032 (mt) cc_final: 0.8712 (pt) REVERT: L 109 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7971 (tp) REVERT: H 21 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6574 (tm) REVERT: A 81 ASP cc_start: 0.8212 (m-30) cc_final: 0.7261 (p0) REVERT: b 24 ARG cc_start: 0.9024 (mtp180) cc_final: 0.6801 (tpt170) REVERT: b 60 LYS cc_start: 0.8951 (pttm) cc_final: 0.8650 (ptpp) REVERT: b 102 ASP cc_start: 0.8791 (p0) cc_final: 0.8579 (p0) REVERT: b 123 ASP cc_start: 0.9187 (t70) cc_final: 0.8891 (t0) REVERT: B 47 ARG cc_start: 0.8367 (ptp90) cc_final: 0.8079 (ptp-110) REVERT: B 61 ASN cc_start: 0.8583 (m-40) cc_final: 0.8230 (m-40) REVERT: B 93 THR cc_start: 0.9265 (OUTLIER) cc_final: 0.8938 (m) REVERT: C 2 LYS cc_start: 0.8538 (tttt) cc_final: 0.6473 (mmtt) REVERT: C 61 ASN cc_start: 0.8068 (m-40) cc_final: 0.7840 (m110) REVERT: C 121 LEU cc_start: 0.8697 (mm) cc_final: 0.8378 (mt) REVERT: C 122 ILE cc_start: 0.8501 (pt) cc_final: 0.7998 (mm) outliers start: 26 outliers final: 23 residues processed: 128 average time/residue: 0.0801 time to fit residues: 13.1611 Evaluate side-chains 132 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 47 HIS Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 41 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 47 HIS ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 ASN 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 = 0.125025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.094884 restraints weight = 7428.591| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.51 r_work: 0.2985 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5741 Z= 0.126 Angle : 0.555 7.543 7815 Z= 0.294 Chirality : 0.047 0.198 921 Planarity : 0.004 0.047 1021 Dihedral : 4.397 28.289 808 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.22 % Allowed : 16.23 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.29), residues: 739 helix: 0.38 (0.56), residues: 96 sheet: -0.20 (0.30), residues: 306 loop : -2.51 (0.26), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 26 TYR 0.010 0.001 TYR H 63 PHE 0.007 0.001 PHE b 94 TRP 0.009 0.001 TRP H 113 HIS 0.009 0.003 HIS L 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 5740) covalent geometry : angle 0.55527 / 0.29 ( 7813) SS BOND : bond 0.00123 / 0.06 ( 1) SS BOND : angle 0.78602 / 0.52 ( 2) hydrogen bonds : bond 0.03760 / 2.63 ( 211) hydrogen bonds : angle 4.59894 / 3.11 ( 582) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1689.11 seconds wall clock time: 29 minutes 41.70 seconds (1781.70 seconds total)