Starting phenix.real_space_refine on Tue Aug 4 23:01:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y7n_72660/08_2026/9y7n_72660.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y7n_72660/08_2026/9y7n_72660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y7n_72660/08_2026/9y7n_72660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y7n_72660/08_2026/9y7n_72660.map" model { file = "/net/cci-nas-00/data/ceres_data/9y7n_72660/08_2026/9y7n_72660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y7n_72660/08_2026/9y7n_72660.cif" } resolution = 2.69 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= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 14 5.16 5 C 2238 2.51 5 N 604 2.21 5 O 714 1.98 5 H 3448 0.53 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: 7018 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 376 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 3316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3316 Classifications: {'peptide': 223} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 211} Chain: "C" Number of atoms: 3326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3326 Classifications: {'peptide': 220} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 205} Time building chain proxies: 1.26, per 1000 atoms: 0.18 Number of scatterers: 7018 At special positions: 0 Unit cell: (60.183, 65.384, 106.992, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 714 8.00 N 604 7.00 C 2238 6.00 H 3448 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 98 " distance=2.03 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 204 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 93 " distance=2.04 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 199 " distance=2.04 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: 0.59 Conformation dependent library (CDL) restraints added in 267.9 milliseconds 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 838 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 12 sheets defined 14.9% alpha, 47.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 91 through 105 Processing helix chain 'A' and resid 119 through 129 removed outlier: 4.198A pdb=" N PHE A 123 " --> pdb=" O LYS A 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.664A pdb=" N ASP B 31 " --> pdb=" O THR B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.693A pdb=" N THR B 93 " --> pdb=" O THR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 195 through 199 removed outlier: 3.910A pdb=" N GLY B 198 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 212 Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.843A pdb=" N VAL C 88 " --> pdb=" O ALA C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 132 removed outlier: 3.826A pdb=" N SER C 132 " --> pdb=" O GLU C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 194 removed outlier: 3.641A pdb=" N HIS C 194 " --> pdb=" O ASP C 190 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12 removed outlier: 4.507A pdb=" N ALA B 33 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.966A pdb=" N VAL B 110 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 128 through 132 removed outlier: 6.315A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 128 through 132 removed outlier: 6.315A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 159 through 162 Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 162 removed outlier: 4.216A pdb=" N TYR B 202 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.660A pdb=" N ASP C 75 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR C 77 " --> pdb=" O SER C 70 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.662A pdb=" N ASP C 110 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C 89 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE C 53 " --> pdb=" O TRP C 40 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU C 42 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N LEU C 51 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.662A pdb=" N ASP C 110 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C 89 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR C 102 " --> pdb=" O GLN C 95 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 119 through 123 removed outlier: 3.557A pdb=" N VAL C 138 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N TYR C 178 " --> pdb=" O ASN C 143 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 158 through 159 184 hydrogen bonds defined for protein. 456 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: 1.39 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3447 1.03 - 1.23: 32 1.23 - 1.43: 1520 1.43 - 1.62: 2081 1.62 - 1.82: 19 Bond restraints: 7099 Sorted by residual: bond pdb=" N LEU C 0 " pdb=" H1 LEU C 0 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" N GLN B 1 " pdb=" H2 GLN B 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" N GLN B 1 " pdb=" H3 GLN B 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N GLN B 1 " pdb=" CA GLN B 1 " ideal model delta sigma weight residual 1.491 1.457 0.034 2.10e-02 2.27e+03 2.63e+00 bond pdb=" N GLN B 1 " pdb=" H1 GLN B 1 " ideal model delta sigma weight residual 0.890 0.860 0.030 2.00e-02 2.50e+03 2.21e+00 ... (remaining 7094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.04: 12764 7.04 - 14.08: 0 14.08 - 21.12: 0 21.12 - 28.17: 1 28.17 - 35.21: 1 Bond angle restraints: 12766 Sorted by residual: angle pdb=" H1 GLN B 1 " pdb=" N GLN B 1 " pdb=" H2 GLN B 1 " ideal model delta sigma weight residual 109.47 74.26 35.21 3.00e+00 1.11e-01 1.38e+02 angle pdb=" H1 GLN B 1 " pdb=" N GLN B 1 " pdb=" H3 GLN B 1 " ideal model delta sigma weight residual 109.47 132.04 -22.57 3.00e+00 1.11e-01 5.66e+01 angle pdb=" N GLU C 148 " pdb=" CA GLU C 148 " pdb=" C GLU C 148 " ideal model delta sigma weight residual 109.15 112.11 -2.96 1.44e+00 4.82e-01 4.22e+00 angle pdb=" CA LEU C 0 " pdb=" N LEU C 0 " pdb=" H1 LEU C 0 " ideal model delta sigma weight residual 120.00 114.05 5.95 3.00e+00 1.11e-01 3.94e+00 angle pdb=" CB MET C 4 " pdb=" CG MET C 4 " pdb=" SD MET C 4 " ideal model delta sigma weight residual 112.70 118.32 -5.62 3.00e+00 1.11e-01 3.51e+00 ... (remaining 12761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 3058 16.17 - 32.34: 230 32.34 - 48.51: 84 48.51 - 64.68: 20 64.68 - 80.85: 5 Dihedral angle restraints: 3397 sinusoidal: 1833 harmonic: 1564 Sorted by residual: dihedral pdb=" CB CYS C 139 " pdb=" SG CYS C 139 " pdb=" SG CYS C 199 " pdb=" CB CYS C 199 " ideal model delta sinusoidal sigma weight residual 93.00 64.03 28.97 1 1.00e+01 1.00e-02 1.20e+01 dihedral pdb=" CB LYS B 218 " pdb=" CG LYS B 218 " pdb=" CD LYS B 218 " pdb=" CE LYS B 218 " ideal model delta sinusoidal sigma weight residual -60.00 -116.79 56.79 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" CA LEU C 38 " pdb=" CB LEU C 38 " pdb=" CG LEU C 38 " pdb=" CD1 LEU C 38 " ideal model delta sinusoidal sigma weight residual 180.00 123.67 56.33 3 1.50e+01 4.44e-03 9.39e+00 ... (remaining 3394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 292 0.026 - 0.052: 162 0.052 - 0.078: 31 0.078 - 0.104: 31 0.104 - 0.130: 27 Chirality restraints: 543 Sorted by residual: chirality pdb=" CA ILE C 53 " pdb=" N ILE C 53 " pdb=" C ILE C 53 " pdb=" CB ILE C 53 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA VAL C 63 " pdb=" N VAL C 63 " pdb=" C VAL C 63 " pdb=" CB VAL C 63 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA ILE C 80 " pdb=" N ILE C 80 " pdb=" C ILE C 80 " pdb=" CB ILE C 80 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 540 not shown) Planarity restraints: 1096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 216 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.03e+00 pdb=" C ASP B 216 " 0.030 2.00e-02 2.50e+03 pdb=" O ASP B 216 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS B 217 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 113 " -0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO A 114 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 114 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 114 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 209 " 0.017 5.00e-02 4.00e+02 2.59e-02 1.08e+00 pdb=" N PRO B 210 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 210 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 210 " 0.014 5.00e-02 4.00e+02 ... (remaining 1093 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.44: 3845 2.44 - 2.98: 15078 2.98 - 3.52: 16771 3.52 - 4.06: 23675 4.06 - 4.60: 33595 Nonbonded interactions: 92964 Sorted by model distance: nonbonded pdb=" H GLN B 6 " pdb="HE22 GLN B 113 " model vdw 1.901 2.100 nonbonded pdb=" HD2 ARG B 69 " pdb="HH11 ARG B 69 " model vdw 1.918 2.270 nonbonded pdb=" H THR B 93 " pdb=" HG1 THR B 93 " model vdw 1.973 2.100 nonbonded pdb=" HD2 ARG C 113 " pdb="HH11 ARG C 113 " model vdw 1.981 2.270 nonbonded pdb=" O ASP A 118 " pdb=" H VAL A 121 " model vdw 1.989 2.450 ... (remaining 92959 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.340 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: 0.030 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.860 Find NCS groups from input model: 0.030 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:7.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 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 : 0.003 0.055 3655 Z= 0.141 Angle : 0.516 5.618 4963 Z= 0.266 Chirality : 0.043 0.130 543 Planarity : 0.004 0.030 645 Dihedral : 12.998 80.846 1306 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.27 % Allowed : 13.20 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.42), residues: 476 helix: 2.30 (1.19), residues: 27 sheet: 0.52 (0.36), residues: 232 loop : 0.35 (0.47), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 82 TYR 0.006 0.001 TYR C 145 PHE 0.008 0.001 PHE C 103 TRP 0.003 0.001 TRP B 162 HIS 0.002 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 3651) covalent geometry : angle 0.51491 / 0.27 ( 4955) SS BOND : bond 0.00503 / 0.32 ( 4) SS BOND : angle 0.86900 / 0.73 ( 8) hydrogen bonds : bond 0.22568 / 16.59 ( 153) hydrogen bonds : angle 9.48478 / 6.95 ( 456) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue SER 127 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Evaluate side-chains 32 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 200 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8376 (mp10) REVERT: C 24 ARG cc_start: 0.7805 (ptp-170) cc_final: 0.7503 (ptm-80) REVERT: C 84 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7848 (mt-10) REVERT: C 148 GLU cc_start: 0.8857 (tp30) cc_final: 0.8037 (tm-30) REVERT: C 166 GLU cc_start: 0.8971 (tt0) cc_final: 0.8364 (tt0) REVERT: C 218 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7845 (mt-10) outliers start: 5 outliers final: 4 residues processed: 31 average time/residue: 1.2287 time to fit residues: 39.2479 Evaluate side-chains 31 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 174 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.0770 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.089765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.067987 restraints weight = 19125.578| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.52 r_work: 0.2847 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.0637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3655 Z= 0.133 Angle : 0.545 4.422 4963 Z= 0.287 Chirality : 0.044 0.130 543 Planarity : 0.004 0.029 645 Dihedral : 4.901 35.402 524 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.76 % Allowed : 14.21 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.41), residues: 476 helix: 1.76 (1.00), residues: 34 sheet: 0.64 (0.35), residues: 232 loop : 0.18 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 66 TYR 0.006 0.001 TYR C 145 PHE 0.009 0.001 PHE C 103 TRP 0.004 0.001 TRP B 111 HIS 0.001 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 ( 3651) covalent geometry : angle 0.54470 / 0.29 ( 4955) SS BOND : bond 0.00650 / 0.40 ( 4) SS BOND : angle 0.87879 / 0.75 ( 8) hydrogen bonds : bond 0.04132 / 2.99 ( 153) hydrogen bonds : angle 6.37853 / 4.62 ( 456) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue SER 127 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Evaluate side-chains 30 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 CYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7958 (p) REVERT: B 200 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8378 (mp10) REVERT: C 24 ARG cc_start: 0.7573 (ptp-170) cc_final: 0.7217 (ptm-80) REVERT: C 84 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8223 (mt-10) REVERT: C 148 GLU cc_start: 0.8786 (tp30) cc_final: 0.7872 (tm-30) REVERT: C 166 GLU cc_start: 0.8947 (tt0) cc_final: 0.8362 (tt0) REVERT: C 218 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7801 (mt-10) outliers start: 3 outliers final: 2 residues processed: 30 average time/residue: 1.3738 time to fit residues: 42.4992 Evaluate side-chains 29 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain C residue 174 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 18 optimal weight: 0.2980 chunk 45 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.090570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.068778 restraints weight = 19051.286| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.54 r_work: 0.2854 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3655 Z= 0.115 Angle : 0.515 4.342 4963 Z= 0.266 Chirality : 0.044 0.131 543 Planarity : 0.003 0.030 645 Dihedral : 4.579 35.630 521 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.78 % Allowed : 13.20 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.41), residues: 476 helix: 1.74 (0.98), residues: 34 sheet: 0.85 (0.36), residues: 231 loop : 0.10 (0.47), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 19 TYR 0.006 0.001 TYR C 92 PHE 0.008 0.001 PHE B 50 TRP 0.006 0.001 TRP B 111 HIS 0.002 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.11 ( 3651) covalent geometry : angle 0.51376 / 0.27 ( 4955) SS BOND : bond 0.00569 / 0.36 ( 4) SS BOND : angle 0.92526 / 0.77 ( 8) hydrogen bonds : bond 0.03218 / 2.32 ( 153) hydrogen bonds : angle 5.55599 / 4.03 ( 456) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue SER 127 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Evaluate side-chains 35 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 98 CYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7919 (p) REVERT: B 200 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8404 (mp10) REVERT: C 84 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8229 (mt-10) REVERT: C 148 GLU cc_start: 0.8826 (tp30) cc_final: 0.7873 (tm-30) REVERT: C 166 GLU cc_start: 0.8910 (tt0) cc_final: 0.8315 (tt0) REVERT: C 218 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7797 (mt-10) outliers start: 7 outliers final: 3 residues processed: 35 average time/residue: 1.1470 time to fit residues: 41.3021 Evaluate side-chains 31 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 174 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.089717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.067966 restraints weight = 19233.373| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.52 r_work: 0.2837 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 3655 Z= 0.152 Angle : 0.531 4.587 4963 Z= 0.274 Chirality : 0.044 0.135 543 Planarity : 0.004 0.044 645 Dihedral : 4.660 35.598 521 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.52 % Allowed : 14.21 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.41), residues: 476 helix: 1.61 (0.97), residues: 34 sheet: 0.92 (0.36), residues: 231 loop : 0.07 (0.47), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 59 TYR 0.013 0.001 TYR C 145 PHE 0.008 0.001 PHE B 50 TRP 0.004 0.001 TRP B 36 HIS 0.002 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.15 ( 3651) covalent geometry : angle 0.52970 / 0.27 ( 4955) SS BOND : bond 0.00633 / 0.39 ( 4) SS BOND : angle 1.02945 / 0.89 ( 8) hydrogen bonds : bond 0.03077 / 2.20 ( 153) hydrogen bonds : angle 5.38395 / 3.89 ( 456) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue SER 127 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Evaluate side-chains 35 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 98 CYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8124 (p) REVERT: B 200 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8408 (mp10) REVERT: C 24 ARG cc_start: 0.7538 (ptp-170) cc_final: 0.7185 (ptm-80) REVERT: C 84 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8279 (mt-10) REVERT: C 148 GLU cc_start: 0.8824 (tp30) cc_final: 0.7878 (tm-30) REVERT: C 166 GLU cc_start: 0.8932 (tt0) cc_final: 0.8334 (tt0) REVERT: C 218 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7881 (mt-10) outliers start: 6 outliers final: 4 residues processed: 35 average time/residue: 1.1899 time to fit residues: 43.0105 Evaluate side-chains 31 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 174 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 40 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 30 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.090084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.068375 restraints weight = 19027.802| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.50 r_work: 0.2845 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3655 Z= 0.127 Angle : 0.520 4.545 4963 Z= 0.267 Chirality : 0.044 0.131 543 Planarity : 0.004 0.028 645 Dihedral : 4.608 35.710 521 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.03 % Allowed : 13.45 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.42), residues: 476 helix: 1.66 (0.97), residues: 34 sheet: 0.96 (0.36), residues: 231 loop : 0.12 (0.47), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 59 TYR 0.012 0.001 TYR C 145 PHE 0.009 0.001 PHE B 50 TRP 0.004 0.001 TRP B 111 HIS 0.002 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 3651) covalent geometry : angle 0.51924 / 0.27 ( 4955) SS BOND : bond 0.00560 / 0.36 ( 4) SS BOND : angle 0.94667 / 0.80 ( 8) hydrogen bonds : bond 0.02872 / 2.06 ( 153) hydrogen bonds : angle 5.17847 / 3.72 ( 456) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue SER 127 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Evaluate side-chains 35 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 MET cc_start: 0.7640 (ppp) cc_final: 0.7367 (ppp) REVERT: B 98 CYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8072 (p) REVERT: B 200 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8418 (mp10) REVERT: C 148 GLU cc_start: 0.8817 (tp30) cc_final: 0.7899 (tm-30) REVERT: C 166 GLU cc_start: 0.8933 (tt0) cc_final: 0.8326 (tt0) REVERT: C 218 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7817 (mt-10) outliers start: 8 outliers final: 6 residues processed: 35 average time/residue: 1.2098 time to fit residues: 43.7800 Evaluate side-chains 34 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 174 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 20 optimal weight: 0.0010 chunk 22 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.090513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.068643 restraints weight = 18968.535| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.52 r_work: 0.2855 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3655 Z= 0.109 Angle : 0.515 5.192 4963 Z= 0.262 Chirality : 0.044 0.132 543 Planarity : 0.003 0.028 645 Dihedral : 4.551 35.584 521 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.78 % Allowed : 14.21 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.42), residues: 476 helix: 1.72 (0.97), residues: 34 sheet: 1.00 (0.36), residues: 231 loop : 0.14 (0.47), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 59 TYR 0.011 0.001 TYR C 145 PHE 0.008 0.001 PHE B 50 TRP 0.005 0.001 TRP B 111 HIS 0.002 0.000 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 ( 3651) covalent geometry : angle 0.51409 / 0.26 ( 4955) SS BOND : bond 0.00510 / 0.33 ( 4) SS BOND : angle 0.86760 / 0.73 ( 8) hydrogen bonds : bond 0.02703 / 1.95 ( 153) hydrogen bonds : angle 5.02131 / 3.60 ( 456) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue SER 127 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Evaluate side-chains 34 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: B 98 CYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8079 (p) REVERT: B 200 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8415 (mp10) REVERT: C 84 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8026 (mt-10) REVERT: C 148 GLU cc_start: 0.8818 (tp30) cc_final: 0.7905 (tm-30) REVERT: C 166 GLU cc_start: 0.8940 (tt0) cc_final: 0.8311 (tt0) REVERT: C 218 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7778 (mt-10) outliers start: 7 outliers final: 5 residues processed: 33 average time/residue: 1.0545 time to fit residues: 35.8441 Evaluate side-chains 31 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 174 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.090602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.068451 restraints weight = 18910.478| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.56 r_work: 0.2838 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3655 Z= 0.120 Angle : 0.524 5.115 4963 Z= 0.266 Chirality : 0.044 0.132 543 Planarity : 0.004 0.032 645 Dihedral : 4.565 35.649 521 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.03 % Allowed : 14.21 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.00 (0.42), residues: 476 helix: 1.75 (0.96), residues: 34 sheet: 1.04 (0.36), residues: 231 loop : 0.14 (0.47), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 82 TYR 0.012 0.001 TYR C 145 PHE 0.008 0.001 PHE B 50 TRP 0.004 0.001 TRP B 111 HIS 0.002 0.000 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 ( 3651) covalent geometry : angle 0.52358 / 0.27 ( 4955) SS BOND : bond 0.00512 / 0.33 ( 4) SS BOND : angle 0.86367 / 0.74 ( 8) hydrogen bonds : bond 0.02694 / 1.93 ( 153) hydrogen bonds : angle 4.94283 / 3.53 ( 456) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue SER 127 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Evaluate side-chains 33 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 98 CYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8088 (p) REVERT: B 200 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8416 (mp10) REVERT: C 84 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8017 (mt-10) REVERT: C 148 GLU cc_start: 0.8839 (tp30) cc_final: 0.7895 (tm-30) REVERT: C 166 GLU cc_start: 0.8957 (tt0) cc_final: 0.8332 (tt0) REVERT: C 218 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7793 (mt-10) outliers start: 8 outliers final: 7 residues processed: 33 average time/residue: 0.9238 time to fit residues: 31.5837 Evaluate side-chains 33 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 174 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 32 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 40 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.090283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.068171 restraints weight = 19041.392| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.55 r_work: 0.2848 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3655 Z= 0.124 Angle : 0.516 4.723 4963 Z= 0.263 Chirality : 0.044 0.137 543 Planarity : 0.004 0.028 645 Dihedral : 4.544 35.748 521 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.03 % Allowed : 14.72 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.42), residues: 476 helix: 1.78 (0.97), residues: 34 sheet: 1.02 (0.36), residues: 231 loop : 0.12 (0.47), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 82 TYR 0.013 0.001 TYR C 145 PHE 0.010 0.001 PHE C 103 TRP 0.004 0.001 TRP B 36 HIS 0.002 0.000 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.12 ( 3651) covalent geometry : angle 0.51465 / 0.26 ( 4955) SS BOND : bond 0.00538 / 0.35 ( 4) SS BOND : angle 0.92638 / 0.79 ( 8) hydrogen bonds : bond 0.02663 / 1.92 ( 153) hydrogen bonds : angle 4.89447 / 3.50 ( 456) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue SER 127 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Evaluate side-chains 32 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 98 CYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8167 (p) REVERT: B 200 GLN cc_start: 0.8970 (mm-40) cc_final: 0.8440 (mp10) REVERT: C 84 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8046 (mt-10) REVERT: C 148 GLU cc_start: 0.8841 (tp30) cc_final: 0.7907 (tm-30) REVERT: C 166 GLU cc_start: 0.8963 (tt0) cc_final: 0.8335 (tt0) REVERT: C 218 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7785 (mt-10) outliers start: 8 outliers final: 7 residues processed: 32 average time/residue: 1.0664 time to fit residues: 35.3902 Evaluate side-chains 32 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 174 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 16 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 45 optimal weight: 0.0980 chunk 27 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.090867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.068953 restraints weight = 18958.019| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.54 r_work: 0.2859 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3655 Z= 0.109 Angle : 0.510 4.559 4963 Z= 0.259 Chirality : 0.044 0.134 543 Planarity : 0.004 0.028 645 Dihedral : 4.494 35.897 521 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.03 % Allowed : 14.72 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.42), residues: 476 helix: 1.80 (0.97), residues: 34 sheet: 1.01 (0.36), residues: 231 loop : 0.15 (0.47), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 82 TYR 0.013 0.001 TYR C 145 PHE 0.009 0.001 PHE C 103 TRP 0.004 0.001 TRP B 111 HIS 0.002 0.000 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 ( 3651) covalent geometry : angle 0.50891 / 0.26 ( 4955) SS BOND : bond 0.00499 / 0.32 ( 4) SS BOND : angle 0.83401 / 0.71 ( 8) hydrogen bonds : bond 0.02546 / 1.84 ( 153) hydrogen bonds : angle 4.81305 / 3.44 ( 456) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue SER 127 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Evaluate side-chains 33 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 34 MET cc_start: 0.7523 (ppp) cc_final: 0.7319 (ppp) REVERT: B 98 CYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8021 (p) REVERT: B 200 GLN cc_start: 0.8968 (mm-40) cc_final: 0.8512 (mp10) REVERT: C 14 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7742 (t) REVERT: C 84 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8036 (mt-10) REVERT: C 148 GLU cc_start: 0.8857 (tp30) cc_final: 0.7911 (tm-30) REVERT: C 166 GLU cc_start: 0.8946 (tt0) cc_final: 0.8339 (tt0) REVERT: C 218 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7784 (mt-10) outliers start: 8 outliers final: 6 residues processed: 33 average time/residue: 1.0076 time to fit residues: 34.5047 Evaluate side-chains 32 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 174 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 42 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.090146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.068204 restraints weight = 18985.888| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.57 r_work: 0.2860 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3655 Z= 0.119 Angle : 0.521 5.716 4963 Z= 0.265 Chirality : 0.044 0.132 543 Planarity : 0.004 0.047 645 Dihedral : 4.510 35.893 521 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.03 % Allowed : 14.97 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.41), residues: 476 helix: 1.79 (0.96), residues: 34 sheet: 1.02 (0.36), residues: 231 loop : 0.15 (0.47), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 82 TYR 0.012 0.001 TYR C 145 PHE 0.009 0.001 PHE B 50 TRP 0.004 0.001 TRP B 36 HIS 0.002 0.000 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.12 ( 3651) covalent geometry : angle 0.51940 / 0.26 ( 4955) SS BOND : bond 0.00563 / 0.35 ( 4) SS BOND : angle 1.01036 / 0.85 ( 8) hydrogen bonds : bond 0.02557 / 1.85 ( 153) hydrogen bonds : angle 4.79282 / 3.42 ( 456) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue SER 127 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Evaluate side-chains 32 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 98 CYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8074 (p) REVERT: B 200 GLN cc_start: 0.8951 (mm-40) cc_final: 0.8497 (mp10) REVERT: C 14 THR cc_start: 0.8092 (OUTLIER) cc_final: 0.7757 (t) REVERT: C 84 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8032 (mt-10) REVERT: C 148 GLU cc_start: 0.8843 (tp30) cc_final: 0.7920 (tm-30) REVERT: C 166 GLU cc_start: 0.8952 (tt0) cc_final: 0.8343 (tt0) REVERT: C 218 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7756 (mt-10) outliers start: 8 outliers final: 6 residues processed: 32 average time/residue: 1.0470 time to fit residues: 34.7389 Evaluate side-chains 32 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 174 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 50.0000 chunk 5 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.090262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.068359 restraints weight = 18902.453| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.53 r_work: 0.2846 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3655 Z= 0.134 Angle : 0.529 5.598 4963 Z= 0.269 Chirality : 0.044 0.133 543 Planarity : 0.004 0.058 645 Dihedral : 4.552 35.955 521 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.03 % Allowed : 14.97 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.00 (0.42), residues: 476 helix: 1.79 (0.96), residues: 34 sheet: 1.03 (0.36), residues: 231 loop : 0.15 (0.47), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 16 TYR 0.015 0.001 TYR C 145 PHE 0.009 0.001 PHE B 50 TRP 0.004 0.001 TRP B 162 HIS 0.002 0.000 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.13 ( 3651) covalent geometry : angle 0.52725 / 0.27 ( 4955) SS BOND : bond 0.00601 / 0.37 ( 4) SS BOND : angle 1.04894 / 0.87 ( 8) hydrogen bonds : bond 0.02652 / 1.89 ( 153) hydrogen bonds : angle 4.80336 / 3.43 ( 456) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2468.83 seconds wall clock time: 42 minutes 27.02 seconds (2547.02 seconds total)