Starting phenix.real_space_refine on Thu Sep 10 19:50:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/23wn_69322/09_2026/23wn_69322_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/23wn_69322/09_2026/23wn_69322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/23wn_69322/09_2026/23wn_69322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/23wn_69322/09_2026/23wn_69322.map" model { file = "/net/cci-nas-00/data/ceres_data/23wn_69322/09_2026/23wn_69322_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/23wn_69322/09_2026/23wn_69322_neut.cif" } resolution = 2.98 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= 0.005 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 Zn 1 6.06 5 S 3 5.16 5 C 1122 2.51 5 N 318 2.21 5 O 339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1783 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1729 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 8, 'TRANS': 216} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 53 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.74, per 1000 atoms: 0.42 Number of scatterers: 1783 At special positions: 0 Unit cell: (57, 51.87, 60.99, 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) Zn 1 29.99 S 3 16.00 O 339 8.00 N 318 7.00 C 1122 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: 0.15 Conformation dependent library (CDL) restraints added in 71.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1601 " pdb="ZN ZN A1601 " - pdb=" NE2 HIS A 119 " pdb="ZN ZN A1601 " - pdb=" NE2 HIS A 123 " 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 424 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 1 sheets defined 67.8% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 42 through 59 removed outlier: 3.858A pdb=" N GLU A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA A 50 " --> pdb=" O MET A 46 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 59 " --> pdb=" O GLU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 85 removed outlier: 3.537A pdb=" N ALA A 72 " --> pdb=" O ASP A 68 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 82 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 132 removed outlier: 3.598A pdb=" N HIS A 123 " --> pdb=" O HIS A 119 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.847A pdb=" N SER A 138 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA A 139 " --> pdb=" O PRO A 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 139' Processing helix chain 'A' and resid 141 through 165 removed outlier: 3.569A pdb=" N LYS A 164 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.769A pdb=" N ARG A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 207 removed outlier: 3.678A pdb=" N VAL A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 239 Proline residue: A 224 - end of helix removed outlier: 3.625A pdb=" N GLU A 227 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 40 removed outlier: 6.237A pdb=" N ASP A 34 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL A 102 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR A 36 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ALA A 104 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N THR A 38 " --> pdb=" O ALA A 104 " (cutoff:3.500A) 102 hydrogen bonds defined for protein. 303 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: 0.27 Time building geometry restraints manager: 0.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 612 1.34 - 1.45: 150 1.45 - 1.57: 1035 1.57 - 1.69: 1 1.69 - 1.80: 6 Bond restraints: 1804 Sorted by residual: bond pdb=" CA ALA A 61 " pdb=" C ALA A 61 " ideal model delta sigma weight residual 1.531 1.500 0.031 1.15e-02 7.56e+03 7.34e+00 bond pdb=" CA ARG A 132 " pdb=" C ARG A 132 " ideal model delta sigma weight residual 1.524 1.493 0.031 1.28e-02 6.10e+03 6.02e+00 bond pdb=" C LYS A 223 " pdb=" O LYS A 223 " ideal model delta sigma weight residual 1.244 1.223 0.021 9.80e-03 1.04e+04 4.63e+00 bond pdb=" CA ALA A 61 " pdb=" CB ALA A 61 " ideal model delta sigma weight residual 1.530 1.510 0.021 9.80e-03 1.04e+04 4.45e+00 bond pdb=" CB PRO A 21 " pdb=" CG PRO A 21 " ideal model delta sigma weight residual 1.492 1.590 -0.098 5.00e-02 4.00e+02 3.83e+00 ... (remaining 1799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 2220 1.56 - 3.12: 169 3.12 - 4.68: 32 4.68 - 6.24: 12 6.24 - 7.81: 8 Bond angle restraints: 2441 Sorted by residual: angle pdb=" N GLU A 28 " pdb=" CA GLU A 28 " pdb=" C GLU A 28 " ideal model delta sigma weight residual 113.97 106.16 7.81 1.28e+00 6.10e-01 3.72e+01 angle pdb=" N LEU A 60 " pdb=" CA LEU A 60 " pdb=" C LEU A 60 " ideal model delta sigma weight residual 113.30 106.37 6.93 1.34e+00 5.57e-01 2.68e+01 angle pdb=" N ARG A 208 " pdb=" CA ARG A 208 " pdb=" C ARG A 208 " ideal model delta sigma weight residual 114.16 107.13 7.03 1.48e+00 4.57e-01 2.26e+01 angle pdb=" N LEU A 163 " pdb=" CA LEU A 163 " pdb=" C LEU A 163 " ideal model delta sigma weight residual 113.41 108.00 5.41 1.22e+00 6.72e-01 1.97e+01 angle pdb=" N GLU A 162 " pdb=" CA GLU A 162 " pdb=" C GLU A 162 " ideal model delta sigma weight residual 113.15 108.49 4.66 1.19e+00 7.06e-01 1.53e+01 ... (remaining 2436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.81: 915 15.81 - 31.61: 131 31.61 - 47.42: 42 47.42 - 63.23: 8 63.23 - 79.03: 4 Dihedral angle restraints: 1100 sinusoidal: 439 harmonic: 661 Sorted by residual: dihedral pdb=" CA PRO A 21 " pdb=" C PRO A 21 " pdb=" N GLY A 22 " pdb=" CA GLY A 22 " ideal model delta harmonic sigma weight residual -180.00 -158.89 -21.11 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA GLY A 188 " pdb=" C GLY A 188 " pdb=" N ARG A 189 " pdb=" CA ARG A 189 " ideal model delta harmonic sigma weight residual 180.00 158.97 21.03 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA VAL A 16 " pdb=" C VAL A 16 " pdb=" N LEU A 17 " pdb=" CA LEU A 17 " ideal model delta harmonic sigma weight residual 180.00 158.97 21.03 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 1097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 191 0.042 - 0.083: 69 0.083 - 0.124: 16 0.124 - 0.166: 6 0.166 - 0.207: 3 Chirality restraints: 285 Sorted by residual: chirality pdb=" CA PRO A 21 " pdb=" N PRO A 21 " pdb=" C PRO A 21 " pdb=" CB PRO A 21 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA GLU A 59 " pdb=" N GLU A 59 " pdb=" C GLU A 59 " pdb=" CB GLU A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.04e-01 chirality pdb=" CA VAL A 39 " pdb=" N VAL A 39 " pdb=" C VAL A 39 " pdb=" CB VAL A 39 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.89e-01 ... (remaining 282 not shown) Planarity restraints: 322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 20 " 0.086 5.00e-02 4.00e+02 1.30e-01 2.72e+01 pdb=" N PRO A 21 " -0.225 5.00e-02 4.00e+02 pdb=" CA PRO A 21 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO A 21 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 135 " -0.073 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO A 136 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO A 136 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 136 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 140 " -0.040 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO A 141 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 141 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 141 " -0.033 5.00e-02 4.00e+02 ... (remaining 319 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 22 2.59 - 3.17: 1508 3.17 - 3.75: 2483 3.75 - 4.32: 3650 4.32 - 4.90: 5766 Nonbonded interactions: 13429 Sorted by model distance: nonbonded pdb=" OE2 GLU A 146 " pdb="ZN ZN A1601 " model vdw 2.017 2.230 nonbonded pdb=" O GLY B 38 " pdb="ZN ZN A1601 " model vdw 2.287 2.230 nonbonded pdb=" O ARG A 76 " pdb=" OG1 THR A 80 " model vdw 2.374 3.040 nonbonded pdb=" O LEU A 135 " pdb=" O PRO A 136 " model vdw 2.419 3.040 nonbonded pdb=" O ARG A 234 " pdb=" OG1 THR A 238 " model vdw 2.434 3.040 ... (remaining 13424 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: 5.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.320 Find NCS groups from input model: 0.010 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:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 0.098 1806 Z= 0.329 Angle : 1.040 7.805 2441 Z= 0.656 Chirality : 0.051 0.207 285 Planarity : 0.011 0.130 322 Dihedral : 16.756 79.033 676 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 1.75 % Allowed : 9.61 % Favored : 88.65 % Rotamer: Outliers : 2.27 % Allowed : 25.00 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.54 (0.51), residues: 229 helix: -2.28 (0.37), residues: 143 sheet: 3.16 (1.20), residues: 22 loop : -4.28 (0.58), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 174 TYR 0.007 0.001 TYR A 70 PHE 0.003 0.001 PHE A 228 TRP 0.002 0.001 TRP A 173 HIS 0.007 0.002 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.33 ( 1804) covalent geometry : angle 1.03983 / 0.66 ( 2441) hydrogen bonds : bond 0.30992 / 20.41 ( 102) hydrogen bonds : angle 8.87830 / 5.95 ( 303) metal coordination : bond 0.00264 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.089 Fit side-chains REVERT: A 171 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6379 (mp0) outliers start: 4 outliers final: 1 residues processed: 36 average time/residue: 0.8594 time to fit residues: 31.2951 Evaluate side-chains 23 residues out of total 176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 171 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 12 optimal weight: 8.9990 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 6 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.189311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.167540 restraints weight = 2193.163| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.34 r_work: 0.3803 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 1806 Z= 0.200 Angle : 0.807 7.827 2441 Z= 0.425 Chirality : 0.048 0.223 285 Planarity : 0.012 0.129 322 Dihedral : 7.817 58.971 264 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 1.31 % Allowed : 7.86 % Favored : 90.83 % Rotamer: Outliers : 5.68 % Allowed : 29.55 % Favored : 64.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.54), residues: 229 helix: -0.65 (0.41), residues: 146 sheet: 3.24 (1.16), residues: 22 loop : -4.06 (0.66), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 186 TYR 0.016 0.002 TYR A 157 PHE 0.010 0.001 PHE A 228 TRP 0.004 0.001 TRP A 173 HIS 0.005 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.20 ( 1804) covalent geometry : angle 0.80696 / 0.42 ( 2441) hydrogen bonds : bond 0.05754 / 3.87 ( 102) hydrogen bonds : angle 4.92180 / 3.35 ( 303) metal coordination : bond 0.00391 / 0.19 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.074 Fit side-chains revert: symmetry clash REVERT: A 128 GLU cc_start: 0.7518 (tp30) cc_final: 0.6948 (tp30) outliers start: 10 outliers final: 3 residues processed: 37 average time/residue: 0.8648 time to fit residues: 32.3761 Evaluate side-chains 23 residues out of total 176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 184 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 11 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.186769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.163859 restraints weight = 2230.447| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.48 r_work: 0.3760 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 1806 Z= 0.197 Angle : 0.768 8.049 2441 Z= 0.399 Chirality : 0.048 0.201 285 Planarity : 0.011 0.130 322 Dihedral : 5.306 19.642 259 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 1.31 % Allowed : 7.86 % Favored : 90.83 % Rotamer: Outliers : 6.25 % Allowed : 30.11 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.55), residues: 229 helix: -0.28 (0.42), residues: 149 sheet: 3.67 (1.05), residues: 22 loop : -4.29 (0.64), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 201 TYR 0.013 0.002 TYR A 157 PHE 0.015 0.002 PHE A 228 TRP 0.003 0.001 TRP A 173 HIS 0.004 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.20 ( 1804) covalent geometry : angle 0.76822 / 0.40 ( 2441) hydrogen bonds : bond 0.05638 / 3.78 ( 102) hydrogen bonds : angle 4.52205 / 3.07 ( 303) metal coordination : bond 0.00469 / 0.23 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.071 Fit side-chains revert: symmetry clash REVERT: A 128 GLU cc_start: 0.7530 (tp30) cc_final: 0.7012 (tp30) outliers start: 11 outliers final: 3 residues processed: 35 average time/residue: 0.8514 time to fit residues: 30.1617 Evaluate side-chains 25 residues out of total 176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 184 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.187367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.165661 restraints weight = 2134.990| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.38 r_work: 0.3795 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 1806 Z= 0.184 Angle : 0.746 7.642 2441 Z= 0.390 Chirality : 0.048 0.203 285 Planarity : 0.011 0.127 322 Dihedral : 5.208 20.120 259 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 1.31 % Allowed : 6.99 % Favored : 91.70 % Rotamer: Outliers : 7.95 % Allowed : 25.57 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.56), residues: 229 helix: -0.05 (0.42), residues: 149 sheet: 3.66 (1.03), residues: 22 loop : -4.14 (0.67), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 99 TYR 0.012 0.002 TYR A 157 PHE 0.013 0.002 PHE A 228 TRP 0.002 0.001 TRP A 173 HIS 0.004 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.18 ( 1804) covalent geometry : angle 0.74578 / 0.39 ( 2441) hydrogen bonds : bond 0.04993 / 3.38 ( 102) hydrogen bonds : angle 4.24852 / 2.87 ( 303) metal coordination : bond 0.00432 / 0.21 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 23 time to evaluate : 0.074 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: A 98 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.6732 (mtt-85) REVERT: A 171 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6986 (mp0) outliers start: 14 outliers final: 7 residues processed: 34 average time/residue: 0.7600 time to fit residues: 26.1799 Evaluate side-chains 33 residues out of total 176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 23 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 39 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.0570 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.188599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.168896 restraints weight = 2149.381| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.13 r_work: 0.3829 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 1806 Z= 0.170 Angle : 0.726 7.405 2441 Z= 0.380 Chirality : 0.046 0.195 285 Planarity : 0.010 0.125 322 Dihedral : 5.001 20.232 259 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 1.31 % Allowed : 6.11 % Favored : 92.58 % Rotamer: Outliers : 7.39 % Allowed : 27.27 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.56), residues: 229 helix: 0.25 (0.42), residues: 149 sheet: 3.60 (1.03), residues: 22 loop : -4.00 (0.70), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 174 TYR 0.011 0.001 TYR A 157 PHE 0.011 0.001 PHE A 228 TRP 0.003 0.001 TRP A 173 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.17 ( 1804) covalent geometry : angle 0.72630 / 0.38 ( 2441) hydrogen bonds : bond 0.04541 / 3.10 ( 102) hydrogen bonds : angle 4.05311 / 2.72 ( 303) metal coordination : bond 0.00298 / 0.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 25 time to evaluate : 0.069 Fit side-chains REVERT: A 82 ILE cc_start: 0.7387 (OUTLIER) cc_final: 0.6992 (mp) REVERT: A 98 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.6835 (mtt-85) REVERT: A 128 GLU cc_start: 0.7584 (tp30) cc_final: 0.7017 (tp30) REVERT: A 171 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6864 (mp0) outliers start: 13 outliers final: 6 residues processed: 35 average time/residue: 0.7064 time to fit residues: 25.0809 Evaluate side-chains 32 residues out of total 176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 23 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 39 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.0980 chunk 4 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 0.0980 chunk 17 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.190989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.169277 restraints weight = 2130.731| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.38 r_work: 0.3842 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 1806 Z= 0.159 Angle : 0.714 7.542 2441 Z= 0.372 Chirality : 0.045 0.196 285 Planarity : 0.010 0.123 322 Dihedral : 4.752 20.310 259 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 1.31 % Allowed : 5.24 % Favored : 93.45 % Rotamer: Outliers : 7.95 % Allowed : 28.98 % Favored : 63.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.57), residues: 229 helix: 0.50 (0.42), residues: 149 sheet: 3.59 (1.05), residues: 22 loop : -3.91 (0.71), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 174 TYR 0.010 0.001 TYR A 157 PHE 0.009 0.001 PHE A 228 TRP 0.002 0.001 TRP A 173 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.16 ( 1804) covalent geometry : angle 0.71354 / 0.37 ( 2441) hydrogen bonds : bond 0.04117 / 2.82 ( 102) hydrogen bonds : angle 3.82704 / 2.55 ( 303) metal coordination : bond 0.00225 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 22 time to evaluate : 0.070 Fit side-chains REVERT: A 98 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.6682 (mtt-85) REVERT: A 128 GLU cc_start: 0.7530 (tp30) cc_final: 0.7004 (tp30) REVERT: A 171 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6491 (mp0) REVERT: A 213 GLU cc_start: 0.6870 (mp0) cc_final: 0.6260 (mp0) outliers start: 14 outliers final: 6 residues processed: 31 average time/residue: 0.7037 time to fit residues: 22.1352 Evaluate side-chains 30 residues out of total 176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain B residue 39 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 5 optimal weight: 0.0570 chunk 21 optimal weight: 0.3980 chunk 0 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 15 optimal weight: 0.0370 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.192215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.170146 restraints weight = 2142.747| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.40 r_work: 0.3853 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 1806 Z= 0.155 Angle : 0.700 7.339 2441 Z= 0.365 Chirality : 0.044 0.198 285 Planarity : 0.010 0.123 322 Dihedral : 4.599 20.368 259 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.87 % Allowed : 6.11 % Favored : 93.01 % Rotamer: Outliers : 6.82 % Allowed : 28.98 % Favored : 64.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.57), residues: 229 helix: 0.64 (0.42), residues: 149 sheet: 3.56 (1.05), residues: 22 loop : -3.87 (0.69), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 174 TYR 0.013 0.001 TYR A 157 PHE 0.009 0.001 PHE A 228 TRP 0.002 0.001 TRP A 173 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.16 ( 1804) covalent geometry : angle 0.70031 / 0.36 ( 2441) hydrogen bonds : bond 0.03961 / 2.71 ( 102) hydrogen bonds : angle 3.75659 / 2.50 ( 303) metal coordination : bond 0.00226 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 22 time to evaluate : 0.070 Fit side-chains REVERT: A 82 ILE cc_start: 0.7091 (OUTLIER) cc_final: 0.6792 (mp) REVERT: A 98 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.6737 (mtt-85) REVERT: A 128 GLU cc_start: 0.7501 (tp30) cc_final: 0.7002 (tp30) REVERT: A 171 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6501 (mp0) REVERT: A 213 GLU cc_start: 0.6881 (mp0) cc_final: 0.6272 (mp0) outliers start: 12 outliers final: 6 residues processed: 31 average time/residue: 0.5843 time to fit residues: 18.4137 Evaluate side-chains 29 residues out of total 176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 39 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 2 optimal weight: 0.0770 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.188220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.165981 restraints weight = 2183.064| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.43 r_work: 0.3809 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 1806 Z= 0.177 Angle : 0.727 6.539 2441 Z= 0.381 Chirality : 0.046 0.212 285 Planarity : 0.010 0.117 322 Dihedral : 4.833 20.500 259 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.87 % Allowed : 6.55 % Favored : 92.58 % Rotamer: Outliers : 8.52 % Allowed : 27.84 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.56), residues: 229 helix: 0.44 (0.42), residues: 150 sheet: 3.61 (1.03), residues: 22 loop : -3.82 (0.71), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 174 TYR 0.014 0.001 TYR A 157 PHE 0.013 0.002 PHE A 228 TRP 0.002 0.001 TRP A 173 HIS 0.002 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.18 ( 1804) covalent geometry : angle 0.72653 / 0.38 ( 2441) hydrogen bonds : bond 0.04603 / 3.10 ( 102) hydrogen bonds : angle 3.95767 / 2.65 ( 303) metal coordination : bond 0.00397 / 0.20 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 21 time to evaluate : 0.071 Fit side-chains REVERT: A 82 ILE cc_start: 0.7210 (OUTLIER) cc_final: 0.6875 (mp) REVERT: A 98 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.6783 (mtt-85) REVERT: A 128 GLU cc_start: 0.7616 (tp30) cc_final: 0.7052 (tp30) REVERT: A 171 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6615 (mp0) outliers start: 15 outliers final: 7 residues processed: 32 average time/residue: 0.6075 time to fit residues: 19.7350 Evaluate side-chains 30 residues out of total 176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 20 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain B residue 39 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 13 optimal weight: 0.0870 chunk 2 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 0.0470 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.189934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.167921 restraints weight = 2134.446| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.41 r_work: 0.3824 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 1806 Z= 0.167 Angle : 0.747 6.124 2441 Z= 0.390 Chirality : 0.045 0.206 285 Planarity : 0.010 0.114 322 Dihedral : 4.726 20.375 259 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.87 % Allowed : 5.24 % Favored : 93.89 % Rotamer: Outliers : 7.39 % Allowed : 28.98 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.56), residues: 229 helix: 0.53 (0.42), residues: 150 sheet: 3.65 (1.04), residues: 22 loop : -3.75 (0.71), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 174 TYR 0.013 0.001 TYR A 157 PHE 0.010 0.001 PHE A 228 TRP 0.001 0.001 TRP A 173 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.17 ( 1804) covalent geometry : angle 0.74670 / 0.39 ( 2441) hydrogen bonds : bond 0.04228 / 2.87 ( 102) hydrogen bonds : angle 3.87552 / 2.59 ( 303) metal coordination : bond 0.00298 / 0.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 21 time to evaluate : 0.057 Fit side-chains REVERT: A 82 ILE cc_start: 0.7143 (OUTLIER) cc_final: 0.6806 (mp) REVERT: A 98 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.6800 (mtt-85) REVERT: A 128 GLU cc_start: 0.7585 (tp30) cc_final: 0.7026 (tp30) REVERT: A 171 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6541 (mp0) REVERT: A 213 GLU cc_start: 0.6799 (mp0) cc_final: 0.6201 (mp0) outliers start: 13 outliers final: 7 residues processed: 30 average time/residue: 0.6237 time to fit residues: 19.0053 Evaluate side-chains 30 residues out of total 176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 20 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 39 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 5 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.185875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.163159 restraints weight = 2151.631| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.34 r_work: 0.3769 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 1806 Z= 0.187 Angle : 0.782 6.257 2441 Z= 0.409 Chirality : 0.047 0.212 285 Planarity : 0.010 0.111 322 Dihedral : 4.882 20.467 259 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.87 % Allowed : 6.99 % Favored : 92.14 % Rotamer: Outliers : 8.52 % Allowed : 28.98 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.56), residues: 229 helix: 0.37 (0.41), residues: 150 sheet: 3.60 (1.02), residues: 22 loop : -3.82 (0.69), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 174 TYR 0.014 0.001 TYR A 157 PHE 0.013 0.002 PHE A 228 TRP 0.002 0.001 TRP A 173 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.19 ( 1804) covalent geometry : angle 0.78181 / 0.41 ( 2441) hydrogen bonds : bond 0.04663 / 3.14 ( 102) hydrogen bonds : angle 4.00818 / 2.68 ( 303) metal coordination : bond 0.00381 / 0.19 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 19 time to evaluate : 0.040 Fit side-chains REVERT: A 82 ILE cc_start: 0.7144 (OUTLIER) cc_final: 0.6820 (mp) REVERT: A 98 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.6805 (mtt-85) REVERT: A 171 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6546 (mp0) outliers start: 15 outliers final: 9 residues processed: 30 average time/residue: 0.5427 time to fit residues: 16.5181 Evaluate side-chains 31 residues out of total 176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 19 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 39 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 21 optimal weight: 0.6980 chunk 19 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.185061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.162076 restraints weight = 2212.735| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.39 r_work: 0.3774 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 1806 Z= 0.179 Angle : 0.781 6.054 2441 Z= 0.409 Chirality : 0.046 0.205 285 Planarity : 0.010 0.108 322 Dihedral : 4.835 20.429 259 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.87 % Allowed : 5.24 % Favored : 93.89 % Rotamer: Outliers : 7.95 % Allowed : 30.11 % Favored : 61.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.56), residues: 229 helix: 0.44 (0.42), residues: 150 sheet: 3.58 (1.03), residues: 22 loop : -3.75 (0.70), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 174 TYR 0.013 0.001 TYR A 157 PHE 0.011 0.001 PHE A 228 TRP 0.001 0.001 TRP A 173 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.18 ( 1804) covalent geometry : angle 0.78065 / 0.41 ( 2441) hydrogen bonds : bond 0.04426 / 2.99 ( 102) hydrogen bonds : angle 3.98374 / 2.66 ( 303) metal coordination : bond 0.00301 / 0.15 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 977.44 seconds wall clock time: 17 minutes 22.67 seconds (1042.67 seconds total)