Starting phenix.real_space_refine on Wed Sep 17 09:05:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9imh_60689/09_2025/9imh_60689.cif Found real_map, /net/cci-nas-00/data/ceres_data/9imh_60689/09_2025/9imh_60689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9imh_60689/09_2025/9imh_60689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9imh_60689/09_2025/9imh_60689.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9imh_60689/09_2025/9imh_60689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9imh_60689/09_2025/9imh_60689.map" } resolution = 4.2 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.855 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 36 5.16 5 C 4842 2.51 5 N 1272 2.21 5 O 1524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7674 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1290 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 9, 'TRANS': 151} Chain: "B" Number of atoms: 1268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1268 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "C" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1290 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 9, 'TRANS': 151} Chain: "D" Number of atoms: 1268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1268 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "E" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1290 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 9, 'TRANS': 151} Chain: "F" Number of atoms: 1268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1268 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 9, 'TRANS': 149} Time building chain proxies: 1.89, per 1000 atoms: 0.25 Number of scatterers: 7674 At special positions: 0 Unit cell: (111.8, 107.9, 61.1, 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 36 16.00 O 1524 8.00 N 1272 7.00 C 4842 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: 0.64 Conformation dependent library (CDL) restraints added in 410.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1800 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 14 sheets defined 23.1% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 3 through 19 Processing helix chain 'A' and resid 85 through 103 Processing helix chain 'B' and resid 3 through 20 Processing helix chain 'B' and resid 85 through 103 Processing helix chain 'C' and resid 3 through 20 removed outlier: 3.564A pdb=" N ASP C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 103 Processing helix chain 'D' and resid 3 through 20 Processing helix chain 'D' and resid 85 through 103 Processing helix chain 'E' and resid 3 through 20 Processing helix chain 'E' and resid 85 through 104 removed outlier: 3.623A pdb=" N GLN E 89 " --> pdb=" O ASP E 85 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY E 104 " --> pdb=" O VAL E 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 20 removed outlier: 3.503A pdb=" N ILE F 7 " --> pdb=" O HIS F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 103 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 53 Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 53 removed outlier: 3.983A pdb=" N MET A 70 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR A 152 " --> pdb=" O MET A 70 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 148 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU A 145 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL A 131 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASN A 147 " --> pdb=" O THR A 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 53 removed outlier: 3.546A pdb=" N TRP B 69 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 51 through 53 removed outlier: 3.543A pdb=" N MET B 70 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR B 152 " --> pdb=" O MET B 70 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B 148 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLU B 145 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL B 131 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASN B 147 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG B 151 " --> pdb=" O ASP B 125 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP B 125 " --> pdb=" O ARG B 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AA6, first strand: chain 'C' and resid 51 through 53 Processing sheet with id=AA7, first strand: chain 'C' and resid 51 through 53 removed outlier: 3.658A pdb=" N MET C 70 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR C 152 " --> pdb=" O MET C 70 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU C 143 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N THR C 133 " --> pdb=" O LEU C 143 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU C 145 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL C 131 " --> pdb=" O GLU C 145 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASN C 147 " --> pdb=" O THR C 129 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AA9, first strand: chain 'D' and resid 51 through 53 removed outlier: 3.594A pdb=" N MET D 70 " --> pdb=" O TYR D 152 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR D 152 " --> pdb=" O MET D 70 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL D 148 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU D 145 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL D 131 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASN D 147 " --> pdb=" O THR D 129 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 51 through 53 Processing sheet with id=AB2, first strand: chain 'E' and resid 51 through 53 removed outlier: 3.633A pdb=" N MET E 70 " --> pdb=" O TYR E 152 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL E 148 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASN E 147 " --> pdb=" O THR E 129 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 107 through 108 removed outlier: 4.531A pdb=" N LEU E 107 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 51 through 53 removed outlier: 3.510A pdb=" N TRP F 69 " --> pdb=" O GLN F 61 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 51 through 53 removed outlier: 3.698A pdb=" N TYR F 152 " --> pdb=" O MET F 70 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL F 148 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL F 78 " --> pdb=" O ALA F 144 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA F 144 " --> pdb=" O VAL F 78 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLU F 145 " --> pdb=" O VAL F 131 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL F 131 " --> pdb=" O GLU F 145 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN F 147 " --> pdb=" O THR F 129 " (cutoff:3.500A) 290 hydrogen bonds defined for protein. 837 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: 0.79 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1335 1.31 - 1.44: 2014 1.44 - 1.56: 4415 1.56 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 7830 Sorted by residual: bond pdb=" CA TYR A 50 " pdb=" C TYR A 50 " ideal model delta sigma weight residual 1.524 1.441 0.083 1.27e-02 6.20e+03 4.22e+01 bond pdb=" CA PHE A 48 " pdb=" CB PHE A 48 " ideal model delta sigma weight residual 1.530 1.439 0.091 1.58e-02 4.01e+03 3.33e+01 bond pdb=" CA PHE B 48 " pdb=" CB PHE B 48 " ideal model delta sigma weight residual 1.530 1.443 0.087 1.58e-02 4.01e+03 3.05e+01 bond pdb=" CA GLU D 47 " pdb=" C GLU D 47 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.31e-02 5.83e+03 2.06e+01 bond pdb=" CA PRO E 49 " pdb=" CB PRO E 49 " ideal model delta sigma weight residual 1.533 1.469 0.064 1.42e-02 4.96e+03 2.04e+01 ... (remaining 7825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 10364 3.04 - 6.09: 214 6.09 - 9.13: 43 9.13 - 12.18: 4 12.18 - 15.22: 1 Bond angle restraints: 10626 Sorted by residual: angle pdb=" N PHE D 28 " pdb=" CA PHE D 28 " pdb=" C PHE D 28 " ideal model delta sigma weight residual 107.62 122.84 -15.22 1.97e+00 2.58e-01 5.97e+01 angle pdb=" C GLU D 82 " pdb=" CA GLU D 82 " pdb=" CB GLU D 82 " ideal model delta sigma weight residual 117.23 107.87 9.36 1.36e+00 5.41e-01 4.74e+01 angle pdb=" CA GLU D 82 " pdb=" C GLU D 82 " pdb=" N LYS D 83 " ideal model delta sigma weight residual 119.98 114.84 5.14 8.50e-01 1.38e+00 3.66e+01 angle pdb=" C PRO C 49 " pdb=" N TYR C 50 " pdb=" CA TYR C 50 " ideal model delta sigma weight residual 122.19 130.29 -8.10 1.41e+00 5.03e-01 3.30e+01 angle pdb=" CA PRO F 49 " pdb=" N PRO F 49 " pdb=" CD PRO F 49 " ideal model delta sigma weight residual 112.00 104.68 7.32 1.40e+00 5.10e-01 2.73e+01 ... (remaining 10621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4217 17.88 - 35.76: 424 35.76 - 53.64: 100 53.64 - 71.52: 14 71.52 - 89.41: 9 Dihedral angle restraints: 4764 sinusoidal: 1956 harmonic: 2808 Sorted by residual: dihedral pdb=" C PHE D 48 " pdb=" N PHE D 48 " pdb=" CA PHE D 48 " pdb=" CB PHE D 48 " ideal model delta harmonic sigma weight residual -122.60 -148.93 26.33 0 2.50e+00 1.60e-01 1.11e+02 dihedral pdb=" N PHE D 48 " pdb=" C PHE D 48 " pdb=" CA PHE D 48 " pdb=" CB PHE D 48 " ideal model delta harmonic sigma weight residual 122.80 147.16 -24.36 0 2.50e+00 1.60e-01 9.50e+01 dihedral pdb=" C PHE F 48 " pdb=" N PHE F 48 " pdb=" CA PHE F 48 " pdb=" CB PHE F 48 " ideal model delta harmonic sigma weight residual -122.60 -141.98 19.38 0 2.50e+00 1.60e-01 6.01e+01 ... (remaining 4761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.232: 1171 0.232 - 0.465: 4 0.465 - 0.697: 4 0.697 - 0.929: 2 0.929 - 1.161: 1 Chirality restraints: 1182 Sorted by residual: chirality pdb=" CA PHE D 48 " pdb=" N PHE D 48 " pdb=" C PHE D 48 " pdb=" CB PHE D 48 " both_signs ideal model delta sigma weight residual False 2.51 1.35 1.16 2.00e-01 2.50e+01 3.37e+01 chirality pdb=" CA PHE F 48 " pdb=" N PHE F 48 " pdb=" C PHE F 48 " pdb=" CB PHE F 48 " both_signs ideal model delta sigma weight residual False 2.51 1.70 0.81 2.00e-01 2.50e+01 1.64e+01 chirality pdb=" CA PHE B 48 " pdb=" N PHE B 48 " pdb=" C PHE B 48 " pdb=" CB PHE B 48 " both_signs ideal model delta sigma weight residual False 2.51 1.78 0.73 2.00e-01 2.50e+01 1.34e+01 ... (remaining 1179 not shown) Planarity restraints: 1392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE F 48 " 0.106 5.00e-02 4.00e+02 1.57e-01 3.95e+01 pdb=" N PRO F 49 " -0.272 5.00e-02 4.00e+02 pdb=" CA PRO F 49 " 0.085 5.00e-02 4.00e+02 pdb=" CD PRO F 49 " 0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 48 " -0.101 5.00e-02 4.00e+02 1.54e-01 3.78e+01 pdb=" N PRO D 49 " 0.266 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 48 " -0.096 5.00e-02 4.00e+02 1.47e-01 3.44e+01 pdb=" N PRO C 49 " 0.254 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " -0.082 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " -0.075 5.00e-02 4.00e+02 ... (remaining 1389 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 445 2.72 - 3.26: 7800 3.26 - 3.81: 11681 3.81 - 4.35: 13461 4.35 - 4.90: 22994 Nonbonded interactions: 56381 Sorted by model distance: nonbonded pdb=" OG1 THR D 84 " pdb=" N ASP D 85 " model vdw 2.171 3.120 nonbonded pdb=" O THR B 39 " pdb=" OH TYR B 50 " model vdw 2.197 3.040 nonbonded pdb=" O THR D 39 " pdb=" OH TYR D 50 " model vdw 2.212 3.040 nonbonded pdb=" O LYS E 83 " pdb=" OG1 THR E 84 " model vdw 2.235 3.040 nonbonded pdb=" O THR A 99 " pdb=" OG1 THR A 103 " model vdw 2.256 3.040 ... (remaining 56376 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 159) selection = chain 'B' selection = (chain 'C' and resid 1 through 159) selection = chain 'D' selection = (chain 'E' and resid 1 through 159) selection = chain 'F' } 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 group one per residue 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: 3.330 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.380 Find NCS groups from input model: 0.130 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 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 0.091 7830 Z= 0.327 Angle : 1.059 15.223 10626 Z= 0.596 Chirality : 0.078 1.161 1182 Planarity : 0.011 0.157 1392 Dihedral : 15.415 89.406 2964 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 3.48 % Allowed : 12.03 % Favored : 84.49 % Rotamer: Outliers : 0.70 % Allowed : 0.93 % Favored : 98.37 % Cbeta Deviations : 0.78 % 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 aren not related in a simple way. whole: -2.10 (0.28), residues: 948 helix: 0.75 (0.38), residues: 198 sheet: -0.50 (0.29), residues: 333 loop : -3.35 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 151 TYR 0.038 0.002 TYR B 109 PHE 0.029 0.002 PHE D 28 TRP 0.009 0.001 TRP D 69 HIS 0.004 0.001 HIS D 3 Details of bonding type rmsd covalent geometry : bond 0.00551 ( 7830) covalent geometry : angle 1.05926 (10626) hydrogen bonds : bond 0.18589 ( 276) hydrogen bonds : angle 7.28098 ( 837) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 319 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASN cc_start: 0.7087 (m-40) cc_final: 0.6795 (m-40) REVERT: A 80 ASP cc_start: 0.7572 (t0) cc_final: 0.6351 (t0) REVERT: B 70 MET cc_start: 0.7965 (tpp) cc_final: 0.7548 (mtt) REVERT: B 88 GLU cc_start: 0.7151 (tp30) cc_final: 0.6902 (tm-30) REVERT: B 113 LYS cc_start: 0.6787 (tppt) cc_final: 0.6370 (tmmt) REVERT: C 45 ILE cc_start: 0.9069 (mp) cc_final: 0.8606 (mt) REVERT: C 69 TRP cc_start: 0.8906 (m100) cc_final: 0.8127 (m100) REVERT: D 46 ARG cc_start: 0.7385 (mpt90) cc_final: 0.5667 (ttt180) REVERT: E 29 ASN cc_start: 0.6881 (m110) cc_final: 0.6442 (m110) REVERT: E 45 ILE cc_start: 0.8224 (mm) cc_final: 0.7903 (tp) REVERT: F 3 HIS cc_start: 0.6935 (m170) cc_final: 0.6719 (m170) REVERT: F 70 MET cc_start: 0.8554 (tpp) cc_final: 0.8204 (mmt) REVERT: F 81 LYS cc_start: 0.7218 (ttpp) cc_final: 0.7015 (ttpt) REVERT: F 108 GLU cc_start: 0.6039 (mm-30) cc_final: 0.5669 (tp30) outliers start: 6 outliers final: 4 residues processed: 323 average time/residue: 0.0858 time to fit residues: 37.2831 Evaluate side-chains 227 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 223 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 29 ASN A 68 GLN B 34 ASN B 89 GLN C 29 ASN C 38 GLN D 34 ASN D 87 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.135937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.127460 restraints weight = 15237.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.129849 restraints weight = 8565.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.131401 restraints weight = 5270.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.132511 restraints weight = 3498.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.133250 restraints weight = 2439.619| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 7830 Z= 0.166 Angle : 0.874 16.983 10626 Z= 0.443 Chirality : 0.050 0.238 1182 Planarity : 0.012 0.171 1392 Dihedral : 6.756 42.995 1056 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 2.43 % Allowed : 11.81 % Favored : 85.76 % Rotamer: Outliers : 0.47 % Allowed : 5.48 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.11 % Twisted General : 0.11 % 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 aren not related in a simple way. whole: -1.74 (0.28), residues: 948 helix: 1.03 (0.37), residues: 198 sheet: 0.02 (0.31), residues: 303 loop : -3.20 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 4 TYR 0.037 0.002 TYR B 109 PHE 0.015 0.002 PHE E 119 TRP 0.006 0.001 TRP F 69 HIS 0.006 0.001 HIS D 3 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 7830) covalent geometry : angle 0.87382 (10626) hydrogen bonds : bond 0.03428 ( 276) hydrogen bonds : angle 4.95108 ( 837) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 279 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASN cc_start: 0.6482 (m110) cc_final: 0.6089 (m-40) REVERT: A 72 LEU cc_start: 0.8734 (tp) cc_final: 0.8445 (tt) REVERT: B 26 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.5441 (pm20) REVERT: B 34 ASN cc_start: 0.6206 (OUTLIER) cc_final: 0.5903 (t0) REVERT: B 70 MET cc_start: 0.8121 (tpp) cc_final: 0.7768 (mtt) REVERT: B 88 GLU cc_start: 0.7872 (tp30) cc_final: 0.7351 (tm-30) REVERT: B 89 GLN cc_start: 0.7728 (tt0) cc_final: 0.7314 (tt0) REVERT: B 126 MET cc_start: 0.7032 (mmm) cc_final: 0.6711 (mmm) REVERT: C 46 ARG cc_start: 0.6831 (ttt180) cc_final: 0.4671 (ttp80) REVERT: C 80 ASP cc_start: 0.7890 (t0) cc_final: 0.7556 (t0) REVERT: D 23 GLN cc_start: 0.7492 (pm20) cc_final: 0.7258 (pm20) REVERT: D 29 ASN cc_start: 0.7947 (p0) cc_final: 0.7741 (p0) REVERT: D 46 ARG cc_start: 0.7091 (mpt90) cc_final: 0.5276 (ttt180) REVERT: D 47 GLU cc_start: 0.5653 (mp0) cc_final: 0.5185 (mp0) REVERT: D 70 MET cc_start: 0.8652 (mmt) cc_final: 0.8375 (mmt) REVERT: D 134 ASP cc_start: 0.8249 (p0) cc_final: 0.8005 (p0) REVERT: E 29 ASN cc_start: 0.6563 (m110) cc_final: 0.6357 (m-40) REVERT: E 85 ASP cc_start: 0.6312 (t0) cc_final: 0.6073 (t0) REVERT: E 141 TYR cc_start: 0.7806 (m-10) cc_final: 0.7138 (m-80) REVERT: F 4 ARG cc_start: 0.8119 (ptp90) cc_final: 0.7878 (ttp80) REVERT: F 70 MET cc_start: 0.8853 (tpp) cc_final: 0.8365 (mtt) REVERT: F 108 GLU cc_start: 0.6224 (mm-30) cc_final: 0.5760 (tp30) REVERT: F 134 ASP cc_start: 0.8551 (p0) cc_final: 0.8201 (p0) outliers start: 4 outliers final: 2 residues processed: 282 average time/residue: 0.0797 time to fit residues: 30.8776 Evaluate side-chains 223 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 219 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 61 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 0 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 68 GLN C 29 ASN C 38 GLN C 147 ASN D 89 GLN E 68 GLN F 87 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.127794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.119916 restraints weight = 15576.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.122189 restraints weight = 8564.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.123692 restraints weight = 5205.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.124736 restraints weight = 3404.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.125441 restraints weight = 2342.386| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 7830 Z= 0.198 Angle : 0.899 19.841 10626 Z= 0.448 Chirality : 0.050 0.232 1182 Planarity : 0.012 0.179 1392 Dihedral : 6.843 43.299 1056 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 2.43 % Allowed : 12.66 % Favored : 84.92 % Rotamer: Outliers : 0.47 % Allowed : 5.13 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.11 % Twisted General : 0.11 % 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 aren not related in a simple way. whole: -1.67 (0.27), residues: 948 helix: 1.00 (0.37), residues: 198 sheet: 0.45 (0.30), residues: 297 loop : -3.38 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 4 TYR 0.031 0.002 TYR B 109 PHE 0.016 0.002 PHE E 71 TRP 0.005 0.001 TRP A 69 HIS 0.004 0.001 HIS F 3 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 7830) covalent geometry : angle 0.89897 (10626) hydrogen bonds : bond 0.03533 ( 276) hydrogen bonds : angle 4.73513 ( 837) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 283 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASN cc_start: 0.6902 (m-40) cc_final: 0.6236 (m-40) REVERT: B 70 MET cc_start: 0.8188 (tpp) cc_final: 0.7733 (mtt) REVERT: B 88 GLU cc_start: 0.7977 (tp30) cc_final: 0.7251 (tm-30) REVERT: B 89 GLN cc_start: 0.8031 (tt0) cc_final: 0.7103 (tt0) REVERT: B 92 LYS cc_start: 0.8103 (mmmt) cc_final: 0.7344 (mmtp) REVERT: B 132 SER cc_start: 0.8186 (t) cc_final: 0.7877 (t) REVERT: C 29 ASN cc_start: 0.7687 (OUTLIER) cc_final: 0.6879 (m110) REVERT: C 50 TYR cc_start: 0.8790 (t80) cc_final: 0.8396 (t80) REVERT: C 80 ASP cc_start: 0.7792 (t0) cc_final: 0.7382 (t0) REVERT: C 91 GLU cc_start: 0.7548 (tm-30) cc_final: 0.6893 (tm-30) REVERT: C 122 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7120 (mm-30) REVERT: D 29 ASN cc_start: 0.8019 (p0) cc_final: 0.7612 (p0) REVERT: D 46 ARG cc_start: 0.7654 (mpt90) cc_final: 0.5194 (ttt180) REVERT: D 47 GLU cc_start: 0.5773 (mp0) cc_final: 0.5290 (mp0) REVERT: D 70 MET cc_start: 0.8435 (mmt) cc_final: 0.8193 (mmt) REVERT: D 82 GLU cc_start: 0.7595 (mp0) cc_final: 0.7347 (mp0) REVERT: D 87 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8285 (mm-40) REVERT: D 134 ASP cc_start: 0.8458 (p0) cc_final: 0.8246 (p0) REVERT: E 13 ASP cc_start: 0.7822 (m-30) cc_final: 0.7390 (m-30) REVERT: F 70 MET cc_start: 0.9064 (tpp) cc_final: 0.8509 (tpp) outliers start: 4 outliers final: 2 residues processed: 286 average time/residue: 0.0844 time to fit residues: 32.9476 Evaluate side-chains 218 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 215 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 52 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 59 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.131695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.123578 restraints weight = 15358.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.125973 restraints weight = 8351.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.127572 restraints weight = 5007.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.128653 restraints weight = 3224.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.129388 restraints weight = 2174.731| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 7830 Z= 0.156 Angle : 0.850 20.033 10626 Z= 0.420 Chirality : 0.048 0.229 1182 Planarity : 0.012 0.181 1392 Dihedral : 6.606 43.061 1056 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 2.53 % Allowed : 12.24 % Favored : 85.23 % Rotamer: Outliers : 0.35 % Allowed : 3.38 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.11 % Twisted General : 0.11 % 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 aren not related in a simple way. whole: -1.60 (0.28), residues: 948 helix: 1.18 (0.37), residues: 198 sheet: -0.03 (0.29), residues: 333 loop : -3.22 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 37 TYR 0.024 0.002 TYR B 109 PHE 0.018 0.002 PHE C 119 TRP 0.013 0.001 TRP E 69 HIS 0.008 0.001 HIS B 3 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 7830) covalent geometry : angle 0.84974 (10626) hydrogen bonds : bond 0.03312 ( 276) hydrogen bonds : angle 4.57996 ( 837) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 272 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ASN cc_start: 0.7247 (m-40) cc_final: 0.6762 (m-40) REVERT: A 45 ILE cc_start: 0.8372 (mp) cc_final: 0.8009 (mt) REVERT: A 109 TYR cc_start: 0.6906 (m-80) cc_final: 0.6699 (m-80) REVERT: B 70 MET cc_start: 0.8272 (tpp) cc_final: 0.7803 (mtt) REVERT: B 80 ASP cc_start: 0.7417 (m-30) cc_final: 0.7143 (m-30) REVERT: B 88 GLU cc_start: 0.7932 (tp30) cc_final: 0.7438 (tm-30) REVERT: B 89 GLN cc_start: 0.7769 (tt0) cc_final: 0.7211 (tt0) REVERT: B 132 SER cc_start: 0.8020 (t) cc_final: 0.7772 (t) REVERT: C 29 ASN cc_start: 0.7358 (m110) cc_final: 0.7106 (m-40) REVERT: C 50 TYR cc_start: 0.8731 (t80) cc_final: 0.8283 (t80) REVERT: C 80 ASP cc_start: 0.7882 (t0) cc_final: 0.7515 (t0) REVERT: C 91 GLU cc_start: 0.7317 (tm-30) cc_final: 0.6875 (tm-30) REVERT: D 11 MET cc_start: 0.8326 (ttm) cc_final: 0.8044 (ttm) REVERT: D 28 PHE cc_start: 0.8154 (p90) cc_final: 0.7734 (p90) REVERT: D 46 ARG cc_start: 0.7610 (mpt90) cc_final: 0.5035 (ttt180) REVERT: D 82 GLU cc_start: 0.7842 (mp0) cc_final: 0.7387 (mp0) REVERT: D 87 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8185 (mm-40) REVERT: D 89 GLN cc_start: 0.7697 (mm110) cc_final: 0.7377 (mm-40) REVERT: D 134 ASP cc_start: 0.8408 (p0) cc_final: 0.8174 (p0) REVERT: E 1 MET cc_start: 0.6652 (ttm) cc_final: 0.5505 (mtp) REVERT: E 2 ASP cc_start: 0.8038 (m-30) cc_final: 0.7759 (m-30) REVERT: E 13 ASP cc_start: 0.7757 (m-30) cc_final: 0.7497 (m-30) REVERT: E 19 MET cc_start: 0.6539 (mmp) cc_final: 0.6286 (mmm) REVERT: E 45 ILE cc_start: 0.8563 (mt) cc_final: 0.8335 (mt) REVERT: E 73 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7275 (mt-10) REVERT: E 74 LEU cc_start: 0.8841 (mp) cc_final: 0.8157 (mt) REVERT: F 4 ARG cc_start: 0.8046 (ptp90) cc_final: 0.7822 (ttm110) REVERT: F 26 GLU cc_start: 0.7340 (pt0) cc_final: 0.6350 (mm-30) REVERT: F 82 GLU cc_start: 0.6864 (mp0) cc_final: 0.6590 (mp0) REVERT: F 88 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7277 (tm-30) outliers start: 3 outliers final: 1 residues processed: 274 average time/residue: 0.0744 time to fit residues: 28.7427 Evaluate side-chains 218 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 11 optimal weight: 0.0050 chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 50 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 overall best weight: 1.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.128582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.120303 restraints weight = 15531.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.122644 restraints weight = 8669.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.124220 restraints weight = 5319.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.125229 restraints weight = 3496.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.126007 restraints weight = 2461.047| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 7830 Z= 0.169 Angle : 0.882 21.693 10626 Z= 0.427 Chirality : 0.050 0.259 1182 Planarity : 0.012 0.188 1392 Dihedral : 6.602 43.172 1056 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 2.43 % Allowed : 12.76 % Favored : 84.81 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.11 % 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 aren not related in a simple way. whole: -1.64 (0.28), residues: 948 helix: 1.20 (0.37), residues: 198 sheet: -0.26 (0.28), residues: 351 loop : -3.17 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 160 TYR 0.022 0.002 TYR B 109 PHE 0.016 0.002 PHE F 48 TRP 0.008 0.001 TRP F 69 HIS 0.006 0.002 HIS D 3 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 7830) covalent geometry : angle 0.88224 (10626) hydrogen bonds : bond 0.03273 ( 276) hydrogen bonds : angle 4.55095 ( 837) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 29 ASN cc_start: 0.7309 (m-40) cc_final: 0.6875 (m-40) REVERT: B 1 MET cc_start: 0.6306 (mpp) cc_final: 0.5973 (mpp) REVERT: B 45 ILE cc_start: 0.8384 (mp) cc_final: 0.8113 (mt) REVERT: B 70 MET cc_start: 0.8373 (tpp) cc_final: 0.8088 (mtt) REVERT: B 80 ASP cc_start: 0.7326 (m-30) cc_final: 0.7094 (m-30) REVERT: B 88 GLU cc_start: 0.8067 (tp30) cc_final: 0.7586 (tm-30) REVERT: B 89 GLN cc_start: 0.7918 (tt0) cc_final: 0.7211 (tt0) REVERT: B 97 ILE cc_start: 0.8730 (tt) cc_final: 0.8504 (tt) REVERT: B 132 SER cc_start: 0.8103 (t) cc_final: 0.7820 (t) REVERT: B 134 ASP cc_start: 0.8147 (p0) cc_final: 0.7712 (p0) REVERT: C 29 ASN cc_start: 0.7431 (m110) cc_final: 0.7123 (m-40) REVERT: C 50 TYR cc_start: 0.8843 (t80) cc_final: 0.8543 (t80) REVERT: C 80 ASP cc_start: 0.7780 (t0) cc_final: 0.7430 (t0) REVERT: C 91 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7186 (tm-30) REVERT: C 122 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7152 (mm-30) REVERT: D 28 PHE cc_start: 0.8180 (p90) cc_final: 0.7682 (p90) REVERT: D 46 ARG cc_start: 0.7603 (mpt90) cc_final: 0.5013 (ttt180) REVERT: D 82 GLU cc_start: 0.7938 (mp0) cc_final: 0.7580 (mp0) REVERT: E 2 ASP cc_start: 0.8154 (m-30) cc_final: 0.7924 (m-30) REVERT: E 13 ASP cc_start: 0.7778 (m-30) cc_final: 0.7347 (m-30) REVERT: F 82 GLU cc_start: 0.6981 (mp0) cc_final: 0.6666 (mp0) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.0745 time to fit residues: 27.1310 Evaluate side-chains 218 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 18 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 0.0070 overall best weight: 2.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 153 GLN C 38 GLN ** D 34 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 = 0.3417 r_free = 0.3417 target = 0.122194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.113806 restraints weight = 15819.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.116163 restraints weight = 8786.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.117746 restraints weight = 5387.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.118758 restraints weight = 3536.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.119536 restraints weight = 2488.806| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 7830 Z= 0.214 Angle : 0.904 15.470 10626 Z= 0.453 Chirality : 0.050 0.209 1182 Planarity : 0.012 0.169 1392 Dihedral : 7.025 43.853 1056 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 2.11 % Allowed : 13.40 % Favored : 84.49 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.11 % Twisted General : 0.11 % 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 aren not related in a simple way. whole: -1.86 (0.27), residues: 948 helix: 0.89 (0.37), residues: 198 sheet: -0.20 (0.29), residues: 321 loop : -3.24 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 4 TYR 0.033 0.002 TYR F 109 PHE 0.013 0.002 PHE A 119 TRP 0.013 0.002 TRP A 69 HIS 0.006 0.001 HIS D 3 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 7830) covalent geometry : angle 0.90415 (10626) hydrogen bonds : bond 0.03515 ( 276) hydrogen bonds : angle 4.64073 ( 837) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ASN cc_start: 0.7665 (m-40) cc_final: 0.7227 (m-40) REVERT: B 19 MET cc_start: 0.6322 (ttt) cc_final: 0.5996 (ttt) REVERT: B 28 PHE cc_start: 0.7607 (p90) cc_final: 0.7275 (p90) REVERT: B 70 MET cc_start: 0.8468 (tpp) cc_final: 0.8198 (mtt) REVERT: B 80 ASP cc_start: 0.7368 (m-30) cc_final: 0.7047 (m-30) REVERT: B 88 GLU cc_start: 0.7929 (tp30) cc_final: 0.7332 (tm-30) REVERT: B 89 GLN cc_start: 0.8033 (tt0) cc_final: 0.7314 (tt0) REVERT: B 132 SER cc_start: 0.8235 (t) cc_final: 0.7956 (t) REVERT: B 134 ASP cc_start: 0.8271 (p0) cc_final: 0.7793 (p0) REVERT: C 29 ASN cc_start: 0.7412 (m110) cc_final: 0.6986 (m-40) REVERT: C 91 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7217 (tm-30) REVERT: C 125 ASP cc_start: 0.7586 (t0) cc_final: 0.7265 (m-30) REVERT: C 141 TYR cc_start: 0.7725 (m-10) cc_final: 0.7325 (m-10) REVERT: D 2 ASP cc_start: 0.7814 (m-30) cc_final: 0.7306 (m-30) REVERT: D 46 ARG cc_start: 0.7618 (mpt90) cc_final: 0.5432 (ttt180) REVERT: D 74 LEU cc_start: 0.9098 (tp) cc_final: 0.8715 (tt) REVERT: D 82 GLU cc_start: 0.7923 (mp0) cc_final: 0.7330 (mp0) REVERT: D 87 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8299 (mm-40) REVERT: D 90 LEU cc_start: 0.9147 (tp) cc_final: 0.8944 (tt) REVERT: D 91 GLU cc_start: 0.6939 (pp20) cc_final: 0.6701 (pp20) REVERT: D 134 ASP cc_start: 0.8633 (p0) cc_final: 0.8370 (p0) REVERT: E 1 MET cc_start: 0.7582 (mtp) cc_final: 0.7084 (mtp) REVERT: E 13 ASP cc_start: 0.8147 (m-30) cc_final: 0.7755 (m-30) REVERT: E 91 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7451 (tm-30) REVERT: F 4 ARG cc_start: 0.8148 (ttp80) cc_final: 0.7915 (ttp80) REVERT: F 26 GLU cc_start: 0.7788 (pt0) cc_final: 0.6325 (mm-30) REVERT: F 82 GLU cc_start: 0.7177 (mp0) cc_final: 0.6906 (mp0) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.0785 time to fit residues: 28.5329 Evaluate side-chains 195 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 16 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 86 optimal weight: 0.0870 chunk 80 optimal weight: 5.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 68 GLN C 38 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.121485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113448 restraints weight = 15668.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.115729 restraints weight = 8655.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117251 restraints weight = 5274.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.118275 restraints weight = 3463.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.118958 restraints weight = 2401.716| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 7830 Z= 0.194 Angle : 0.926 23.758 10626 Z= 0.448 Chirality : 0.050 0.199 1182 Planarity : 0.012 0.191 1392 Dihedral : 7.090 46.565 1056 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 2.00 % Allowed : 13.19 % Favored : 84.81 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.11 % Twisted General : 0.11 % 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 aren not related in a simple way. whole: -1.80 (0.27), residues: 948 helix: 1.27 (0.37), residues: 189 sheet: -0.30 (0.29), residues: 321 loop : -3.16 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 4 TYR 0.025 0.002 TYR F 109 PHE 0.014 0.002 PHE A 48 TRP 0.011 0.001 TRP A 69 HIS 0.007 0.002 HIS D 3 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 7830) covalent geometry : angle 0.92553 (10626) hydrogen bonds : bond 0.03448 ( 276) hydrogen bonds : angle 4.60549 ( 837) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 THR cc_start: 0.8641 (p) cc_final: 0.8413 (p) REVERT: A 7 ILE cc_start: 0.8843 (mt) cc_final: 0.8556 (mt) REVERT: A 29 ASN cc_start: 0.7795 (m-40) cc_final: 0.7400 (m-40) REVERT: A 70 MET cc_start: 0.7235 (mtp) cc_final: 0.6960 (mmt) REVERT: B 17 LYS cc_start: 0.7750 (ptmt) cc_final: 0.7271 (mmmt) REVERT: B 19 MET cc_start: 0.6371 (ttt) cc_final: 0.5955 (ttt) REVERT: B 89 GLN cc_start: 0.7927 (tt0) cc_final: 0.7333 (tt0) REVERT: B 132 SER cc_start: 0.8309 (t) cc_final: 0.8074 (t) REVERT: B 134 ASP cc_start: 0.8324 (p0) cc_final: 0.7857 (p0) REVERT: C 91 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7213 (tm-30) REVERT: C 125 ASP cc_start: 0.7424 (t0) cc_final: 0.7039 (m-30) REVERT: D 11 MET cc_start: 0.8656 (ttm) cc_final: 0.8357 (ttm) REVERT: D 23 GLN cc_start: 0.7747 (pm20) cc_final: 0.7404 (pm20) REVERT: D 46 ARG cc_start: 0.7607 (mpt90) cc_final: 0.5424 (ttt180) REVERT: D 74 LEU cc_start: 0.9300 (tp) cc_final: 0.8446 (tt) REVERT: D 82 GLU cc_start: 0.7881 (mp0) cc_final: 0.7340 (mp0) REVERT: D 87 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8286 (mm-40) REVERT: D 90 LEU cc_start: 0.9194 (tp) cc_final: 0.8964 (tp) REVERT: D 134 ASP cc_start: 0.8666 (p0) cc_final: 0.8417 (p0) REVERT: E 13 ASP cc_start: 0.8104 (m-30) cc_final: 0.7746 (m-30) REVERT: E 91 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7463 (tm-30) REVERT: F 4 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7705 (ttp80) REVERT: F 70 MET cc_start: 0.8908 (mmt) cc_final: 0.8658 (mmt) REVERT: F 82 GLU cc_start: 0.7137 (mp0) cc_final: 0.6896 (mp0) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.0788 time to fit residues: 26.4558 Evaluate side-chains 196 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 57 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 62 optimal weight: 7.9990 chunk 24 optimal weight: 0.4980 chunk 91 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 81 optimal weight: 0.0070 chunk 51 optimal weight: 0.0870 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 38 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.129802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.121805 restraints weight = 15228.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.124063 restraints weight = 8570.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.125557 restraints weight = 5287.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.126620 restraints weight = 3515.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.127371 restraints weight = 2442.114| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 7830 Z= 0.141 Angle : 0.846 18.751 10626 Z= 0.414 Chirality : 0.048 0.194 1182 Planarity : 0.011 0.175 1392 Dihedral : 6.676 48.006 1056 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 1.79 % Allowed : 13.71 % Favored : 84.49 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.11 % Twisted General : 0.11 % 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 aren not related in a simple way. whole: -1.63 (0.28), residues: 948 helix: 1.12 (0.36), residues: 195 sheet: -0.11 (0.29), residues: 327 loop : -3.07 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 4 TYR 0.021 0.002 TYR F 109 PHE 0.017 0.002 PHE B 28 TRP 0.018 0.001 TRP A 69 HIS 0.009 0.002 HIS D 3 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 7830) covalent geometry : angle 0.84644 (10626) hydrogen bonds : bond 0.03066 ( 276) hydrogen bonds : angle 4.63009 ( 837) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 THR cc_start: 0.8709 (p) cc_final: 0.8377 (p) REVERT: B 1 MET cc_start: 0.6080 (mpp) cc_final: 0.5797 (mpp) REVERT: B 17 LYS cc_start: 0.7700 (ptmt) cc_final: 0.7247 (mmmt) REVERT: B 89 GLN cc_start: 0.7956 (tt0) cc_final: 0.7634 (tt0) REVERT: B 132 SER cc_start: 0.8160 (t) cc_final: 0.7959 (t) REVERT: C 45 ILE cc_start: 0.9130 (mt) cc_final: 0.8921 (mt) REVERT: C 70 MET cc_start: 0.8016 (mmm) cc_final: 0.7719 (mmt) REVERT: C 91 GLU cc_start: 0.7537 (tm-30) cc_final: 0.6954 (tm-30) REVERT: D 11 MET cc_start: 0.8590 (ttm) cc_final: 0.8277 (ttm) REVERT: D 22 SER cc_start: 0.8083 (p) cc_final: 0.7661 (p) REVERT: D 26 GLU cc_start: 0.6886 (pt0) cc_final: 0.5797 (mm-30) REVERT: D 28 PHE cc_start: 0.7707 (p90) cc_final: 0.7221 (p90) REVERT: D 38 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7527 (mm-40) REVERT: D 46 ARG cc_start: 0.7502 (mpt90) cc_final: 0.5291 (ttt180) REVERT: D 70 MET cc_start: 0.8376 (mmt) cc_final: 0.7843 (mmt) REVERT: D 74 LEU cc_start: 0.9221 (tp) cc_final: 0.8591 (tt) REVERT: D 82 GLU cc_start: 0.7811 (mp0) cc_final: 0.7296 (mp0) REVERT: D 87 GLN cc_start: 0.8581 (mm-40) cc_final: 0.8312 (mm-40) REVERT: E 13 ASP cc_start: 0.7827 (m-30) cc_final: 0.7412 (m-30) REVERT: E 91 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7241 (tm-30) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.0722 time to fit residues: 27.2945 Evaluate side-chains 224 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 62 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 115 ASN C 38 GLN ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 29 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.121585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.113649 restraints weight = 15634.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.115903 restraints weight = 8824.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.117400 restraints weight = 5440.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.118429 restraints weight = 3598.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.119111 restraints weight = 2496.630| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 7830 Z= 0.205 Angle : 0.964 28.208 10626 Z= 0.459 Chirality : 0.050 0.197 1182 Planarity : 0.012 0.203 1392 Dihedral : 6.932 49.476 1056 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 1.79 % Allowed : 13.29 % Favored : 84.92 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.11 % Twisted General : 0.11 % 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 aren not related in a simple way. whole: -1.78 (0.27), residues: 948 helix: 1.15 (0.37), residues: 195 sheet: -0.25 (0.29), residues: 321 loop : -3.16 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 4 TYR 0.029 0.002 TYR F 109 PHE 0.018 0.002 PHE B 28 TRP 0.018 0.002 TRP A 69 HIS 0.009 0.002 HIS E 3 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 7830) covalent geometry : angle 0.96371 (10626) hydrogen bonds : bond 0.03632 ( 276) hydrogen bonds : angle 4.73911 ( 837) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7719 (ptmt) cc_final: 0.7282 (mmmt) REVERT: B 89 GLN cc_start: 0.8070 (tt0) cc_final: 0.7783 (tt0) REVERT: B 134 ASP cc_start: 0.8231 (p0) cc_final: 0.7828 (p0) REVERT: C 80 ASP cc_start: 0.7870 (t0) cc_final: 0.7510 (t0) REVERT: C 91 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7204 (tm-30) REVERT: C 124 THR cc_start: 0.8952 (m) cc_final: 0.8745 (m) REVERT: C 125 ASP cc_start: 0.7241 (t0) cc_final: 0.6983 (m-30) REVERT: D 2 ASP cc_start: 0.7905 (m-30) cc_final: 0.7452 (m-30) REVERT: D 19 MET cc_start: 0.8066 (ttp) cc_final: 0.7222 (ttt) REVERT: D 28 PHE cc_start: 0.7854 (p90) cc_final: 0.7403 (p90) REVERT: D 46 ARG cc_start: 0.7465 (mpt90) cc_final: 0.5840 (ttt180) REVERT: D 74 LEU cc_start: 0.9324 (tp) cc_final: 0.8702 (tt) REVERT: D 82 GLU cc_start: 0.8008 (mp0) cc_final: 0.7496 (mp0) REVERT: D 87 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8352 (mm-40) REVERT: D 134 ASP cc_start: 0.8760 (p0) cc_final: 0.8483 (p0) REVERT: E 13 ASP cc_start: 0.8119 (m-30) cc_final: 0.7782 (m-30) REVERT: E 20 ASP cc_start: 0.7676 (p0) cc_final: 0.7463 (p0) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.0653 time to fit residues: 23.1036 Evaluate side-chains 201 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 74 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.125834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.117567 restraints weight = 15325.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.120040 restraints weight = 8472.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.121575 restraints weight = 5131.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.122684 restraints weight = 3372.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.123383 restraints weight = 2303.478| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 7830 Z= 0.157 Angle : 0.905 26.597 10626 Z= 0.430 Chirality : 0.049 0.183 1182 Planarity : 0.012 0.197 1392 Dihedral : 6.813 52.717 1056 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 1.69 % Allowed : 13.71 % Favored : 84.60 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.11 % Twisted General : 0.11 % 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 aren not related in a simple way. whole: -1.70 (0.28), residues: 948 helix: 1.14 (0.37), residues: 195 sheet: -0.35 (0.29), residues: 315 loop : -2.91 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 4 TYR 0.021 0.002 TYR F 109 PHE 0.025 0.002 PHE B 28 TRP 0.016 0.001 TRP A 69 HIS 0.010 0.002 HIS D 3 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 7830) covalent geometry : angle 0.90539 (10626) hydrogen bonds : bond 0.03235 ( 276) hydrogen bonds : angle 4.72741 ( 837) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.7394 (mmt) cc_final: 0.7119 (mmt) REVERT: B 1 MET cc_start: 0.6061 (mpp) cc_final: 0.5459 (mpp) REVERT: B 17 LYS cc_start: 0.7711 (ptmt) cc_final: 0.7274 (mmmt) REVERT: B 89 GLN cc_start: 0.8081 (tt0) cc_final: 0.7734 (tt0) REVERT: B 132 SER cc_start: 0.8149 (t) cc_final: 0.7880 (t) REVERT: B 134 ASP cc_start: 0.8228 (p0) cc_final: 0.7791 (p0) REVERT: C 45 ILE cc_start: 0.8995 (mt) cc_final: 0.8709 (mt) REVERT: C 70 MET cc_start: 0.8096 (mmm) cc_final: 0.7773 (mmt) REVERT: C 80 ASP cc_start: 0.7859 (t0) cc_final: 0.7483 (t0) REVERT: C 91 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7170 (tm-30) REVERT: D 1 MET cc_start: 0.6912 (mpp) cc_final: 0.6481 (mpp) REVERT: D 2 ASP cc_start: 0.7787 (m-30) cc_final: 0.7310 (m-30) REVERT: D 19 MET cc_start: 0.7912 (ttp) cc_final: 0.7025 (ttt) REVERT: D 28 PHE cc_start: 0.7627 (p90) cc_final: 0.7324 (p90) REVERT: D 46 ARG cc_start: 0.7667 (mpt90) cc_final: 0.5651 (ttt180) REVERT: D 70 MET cc_start: 0.8374 (mmt) cc_final: 0.7849 (mmt) REVERT: D 74 LEU cc_start: 0.9296 (tp) cc_final: 0.8646 (tt) REVERT: D 82 GLU cc_start: 0.7786 (mp0) cc_final: 0.7242 (mp0) REVERT: D 87 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8289 (mm-40) REVERT: E 13 ASP cc_start: 0.7924 (m-30) cc_final: 0.7555 (m-30) REVERT: E 92 LYS cc_start: 0.7074 (mmtp) cc_final: 0.6856 (mttt) REVERT: F 26 GLU cc_start: 0.7282 (pt0) cc_final: 0.6328 (mm-30) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.0672 time to fit residues: 24.7727 Evaluate side-chains 206 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 68 optimal weight: 0.0670 chunk 17 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 overall best weight: 2.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 38 GLN D 3 HIS ** D 34 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 = 0.3366 r_free = 0.3366 target = 0.118277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109981 restraints weight = 15818.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112350 restraints weight = 8785.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.113931 restraints weight = 5357.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.114983 restraints weight = 3511.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115774 restraints weight = 2434.270| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.5761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 7830 Z= 0.249 Angle : 0.993 25.224 10626 Z= 0.482 Chirality : 0.052 0.180 1182 Planarity : 0.012 0.193 1392 Dihedral : 7.311 54.123 1056 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 1.48 % Allowed : 14.56 % Favored : 83.97 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.11 % Twisted General : 0.11 % 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 aren not related in a simple way. whole: -2.02 (0.27), residues: 948 helix: 1.12 (0.37), residues: 195 sheet: -0.51 (0.28), residues: 321 loop : -3.31 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 4 TYR 0.046 0.002 TYR B 109 PHE 0.017 0.003 PHE E 48 TRP 0.013 0.002 TRP A 69 HIS 0.008 0.002 HIS E 3 Details of bonding type rmsd covalent geometry : bond 0.00605 ( 7830) covalent geometry : angle 0.99323 (10626) hydrogen bonds : bond 0.03680 ( 276) hydrogen bonds : angle 4.80635 ( 837) =============================================================================== Job complete usr+sys time: 1280.49 seconds wall clock time: 22 minutes 57.66 seconds (1377.66 seconds total)