Starting phenix.real_space_refine on Fri Aug 22 15:41:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j6f_36003/08_2025/8j6f_36003.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6f_36003/08_2025/8j6f_36003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j6f_36003/08_2025/8j6f_36003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6f_36003/08_2025/8j6f_36003.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j6f_36003/08_2025/8j6f_36003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6f_36003/08_2025/8j6f_36003.map" } resolution = 3.3 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1592 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 2443 2.51 5 N 657 2.21 5 O 758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3870 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1590 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1615 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 197} Chain: "I" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 571 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 5, 'TRANS': 60} Chain breaks: 3 Chain: "B" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 80 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.42, per 1000 atoms: 0.37 Number of scatterers: 3870 At special positions: 0 Unit cell: (54.12, 64.78, 107.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 758 8.00 N 657 7.00 C 2443 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG I 401 " - " ASN I 221 " Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 157.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 934 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 12 sheets defined 1.8% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'H' and resid 73 through 76 Processing helix chain 'H' and resid 191 through 195 removed outlier: 3.625A pdb=" N SER H 194 " --> pdb=" O PRO H 191 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU H 195 " --> pdb=" O SER H 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 191 through 195' Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 59 removed outlier: 4.322A pdb=" N TRP H 37 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N TRP H 35 " --> pdb=" O TYR H 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA H 92 " --> pdb=" O VAL H 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 126 through 130 removed outlier: 6.174A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 126 through 130 removed outlier: 6.174A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 159 through 160 removed outlier: 4.639A pdb=" N TYR H 200 " --> pdb=" O VAL H 217 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 7 removed outlier: 4.163A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.382A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.620A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 114 through 115 removed outlier: 3.732A pdb=" N CYS L 134 " --> pdb=" O SER L 177 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 144 through 148 removed outlier: 4.265A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 220 through 223 removed outlier: 5.556A pdb=" N ASN I 221 " --> pdb=" O GLN I 239 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLN I 239 " --> pdb=" O ASN I 221 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR I 237 " --> pdb=" O THR I 223 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 268 through 269 removed outlier: 3.623A pdb=" N GLU I 254 " --> pdb=" O ARG I 293 " (cutoff:3.500A) 108 hydrogen bonds defined for protein. 270 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: 0.56 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1065 1.33 - 1.45: 757 1.45 - 1.57: 2127 1.57 - 1.69: 1 1.69 - 1.81: 16 Bond restraints: 3966 Sorted by residual: bond pdb=" C ALA H 101 " pdb=" N ARG H 102 " ideal model delta sigma weight residual 1.332 1.297 0.036 1.40e-02 5.10e+03 6.49e+00 bond pdb=" CG LEU L 94 " pdb=" CD2 LEU L 94 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.27e+00 bond pdb=" SD MET H 106 " pdb=" CE MET H 106 " ideal model delta sigma weight residual 1.791 1.742 0.049 2.50e-02 1.60e+03 3.92e+00 bond pdb=" CG GLN L 90 " pdb=" CD GLN L 90 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.58e+00 bond pdb=" CA THR H 157 " pdb=" CB THR H 157 " ideal model delta sigma weight residual 1.539 1.630 -0.090 4.88e-02 4.20e+02 3.43e+00 ... (remaining 3961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 5051 1.92 - 3.83: 286 3.83 - 5.75: 42 5.75 - 7.66: 14 7.66 - 9.58: 9 Bond angle restraints: 5402 Sorted by residual: angle pdb=" C TYR L 50 " pdb=" N THR L 51 " pdb=" CA THR L 51 " ideal model delta sigma weight residual 121.54 129.30 -7.76 1.91e+00 2.74e-01 1.65e+01 angle pdb=" CB LYS H 215 " pdb=" CG LYS H 215 " pdb=" CD LYS H 215 " ideal model delta sigma weight residual 111.30 119.08 -7.78 2.30e+00 1.89e-01 1.14e+01 angle pdb=" C TRP L 148 " pdb=" N LYS L 149 " pdb=" CA LYS L 149 " ideal model delta sigma weight residual 121.54 127.86 -6.32 1.91e+00 2.74e-01 1.10e+01 angle pdb=" N PHE H 152 " pdb=" CA PHE H 152 " pdb=" C PHE H 152 " ideal model delta sigma weight residual 109.81 117.10 -7.29 2.21e+00 2.05e-01 1.09e+01 angle pdb=" N GLU H 154 " pdb=" CA GLU H 154 " pdb=" C GLU H 154 " ideal model delta sigma weight residual 108.97 114.84 -5.87 1.82e+00 3.02e-01 1.04e+01 ... (remaining 5397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 2128 17.44 - 34.88: 203 34.88 - 52.32: 40 52.32 - 69.76: 5 69.76 - 87.19: 4 Dihedral angle restraints: 2380 sinusoidal: 935 harmonic: 1445 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 148.64 -55.64 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CA GLU I 296 " pdb=" C GLU I 296 " pdb=" N GLU I 297 " pdb=" CA GLU I 297 " ideal model delta harmonic sigma weight residual 180.00 -151.29 -28.71 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA PRO H 155 " pdb=" C PRO H 155 " pdb=" N VAL H 156 " pdb=" CA VAL H 156 " ideal model delta harmonic sigma weight residual -180.00 -154.76 -25.24 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 2377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 373 0.045 - 0.090: 155 0.090 - 0.135: 60 0.135 - 0.180: 17 0.180 - 0.225: 6 Chirality restraints: 611 Sorted by residual: chirality pdb=" CA PHE H 152 " pdb=" N PHE H 152 " pdb=" C PHE H 152 " pdb=" CB PHE H 152 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB VAL B 111 " pdb=" CA VAL B 111 " pdb=" CG1 VAL B 111 " pdb=" CG2 VAL B 111 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CG LEU H 20 " pdb=" CB LEU H 20 " pdb=" CD1 LEU H 20 " pdb=" CD2 LEU H 20 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 608 not shown) Planarity restraints: 684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN H 61 " -0.083 5.00e-02 4.00e+02 1.25e-01 2.49e+01 pdb=" N PRO H 62 " 0.216 5.00e-02 4.00e+02 pdb=" CA PRO H 62 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO H 62 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " 0.075 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO L 80 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 154 " -0.061 5.00e-02 4.00e+02 9.22e-02 1.36e+01 pdb=" N PRO H 155 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO H 155 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO H 155 " -0.051 5.00e-02 4.00e+02 ... (remaining 681 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 458 2.75 - 3.29: 3545 3.29 - 3.82: 6540 3.82 - 4.36: 7591 4.36 - 4.90: 13565 Nonbonded interactions: 31699 Sorted by model distance: nonbonded pdb=" OG SER H 36 " pdb=" OG SER H 99 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR L 96 " pdb=" O PHE I 298 " model vdw 2.230 3.040 nonbonded pdb=" O ASP H 90 " pdb=" OH TYR H 94 " model vdw 2.265 3.040 nonbonded pdb=" O PRO H 173 " pdb=" OG SER L 162 " model vdw 2.273 3.040 nonbonded pdb=" O ILE L 106 " pdb=" NE2 GLN L 166 " model vdw 2.309 3.120 ... (remaining 31694 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=0.00 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: 4.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.340 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 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 : 0.009 0.099 3971 Z= 0.351 Angle : 1.062 9.576 5413 Z= 0.551 Chirality : 0.060 0.225 611 Planarity : 0.011 0.125 683 Dihedral : 14.303 87.194 1434 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.18 (0.37), residues: 480 helix: -5.48 (0.27), residues: 6 sheet: -2.43 (0.34), residues: 204 loop : -1.69 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 67 TYR 0.036 0.004 TYR I 249 PHE 0.054 0.005 PHE I 298 TRP 0.018 0.003 TRP I 238 HIS 0.010 0.002 HIS I 275 Details of bonding type rmsd covalent geometry : bond 0.00862 ( 3966) covalent geometry : angle 1.05952 ( 5402) SS BOND : bond 0.00604 ( 4) SS BOND : angle 1.67586 ( 8) hydrogen bonds : bond 0.27058 ( 95) hydrogen bonds : angle 13.00326 ( 270) link_NAG-ASN : bond 0.00103 ( 1) link_NAG-ASN : angle 2.71189 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.158 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0858 time to fit residues: 6.0892 Evaluate side-chains 46 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.0980 chunk 26 optimal weight: 0.0170 chunk 2 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 overall best weight: 0.2018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 275 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.191624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.157856 restraints weight = 4056.038| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.30 r_work: 0.3755 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3971 Z= 0.137 Angle : 0.691 12.642 5413 Z= 0.351 Chirality : 0.045 0.157 611 Planarity : 0.008 0.076 683 Dihedral : 6.100 23.962 552 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.46 % Allowed : 8.88 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.95 (0.38), residues: 480 helix: -5.47 (0.27), residues: 6 sheet: -2.26 (0.33), residues: 226 loop : -1.41 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 293 TYR 0.015 0.001 TYR I 249 PHE 0.012 0.002 PHE I 298 TRP 0.015 0.002 TRP I 306 HIS 0.002 0.001 HIS I 275 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 3966) covalent geometry : angle 0.68924 ( 5402) SS BOND : bond 0.00358 ( 4) SS BOND : angle 1.14681 ( 8) hydrogen bonds : bond 0.04445 ( 95) hydrogen bonds : angle 8.59668 ( 270) link_NAG-ASN : bond 0.00282 ( 1) link_NAG-ASN : angle 1.17097 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.202 Fit side-chains REVERT: L 24 ARG cc_start: 0.6461 (mtp180) cc_final: 0.6158 (mtp-110) outliers start: 2 outliers final: 0 residues processed: 53 average time/residue: 0.0623 time to fit residues: 4.2033 Evaluate side-chains 47 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 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 = 0.4235 r_free = 0.4235 target = 0.188464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.154267 restraints weight = 4027.370| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.29 r_work: 0.3706 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 3971 Z= 0.206 Angle : 0.694 7.453 5413 Z= 0.351 Chirality : 0.045 0.148 611 Planarity : 0.007 0.065 683 Dihedral : 5.889 24.950 552 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 0.91 % Allowed : 12.98 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.70 (0.38), residues: 480 helix: -5.44 (0.28), residues: 6 sheet: -2.02 (0.35), residues: 209 loop : -1.40 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 61 TYR 0.016 0.002 TYR I 249 PHE 0.015 0.002 PHE L 139 TRP 0.025 0.002 TRP I 306 HIS 0.005 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 3966) covalent geometry : angle 0.69307 ( 5402) SS BOND : bond 0.00435 ( 4) SS BOND : angle 1.06061 ( 8) hydrogen bonds : bond 0.03763 ( 95) hydrogen bonds : angle 7.73157 ( 270) link_NAG-ASN : bond 0.00274 ( 1) link_NAG-ASN : angle 0.84192 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.149 Fit side-chains REVERT: L 24 ARG cc_start: 0.6500 (mtp180) cc_final: 0.6215 (mtp-110) outliers start: 4 outliers final: 3 residues processed: 54 average time/residue: 0.0718 time to fit residues: 4.9733 Evaluate side-chains 53 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain L residue 132 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 0.1980 chunk 3 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 chunk 13 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 42 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.189495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.155554 restraints weight = 3999.297| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.28 r_work: 0.3734 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3971 Z= 0.164 Angle : 0.647 6.507 5413 Z= 0.328 Chirality : 0.044 0.149 611 Planarity : 0.007 0.059 683 Dihedral : 5.642 25.042 552 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 1.14 % Allowed : 14.58 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.55 (0.39), residues: 480 helix: -5.42 (0.28), residues: 6 sheet: -1.98 (0.35), residues: 212 loop : -1.23 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 250 TYR 0.018 0.002 TYR L 87 PHE 0.020 0.002 PHE I 298 TRP 0.011 0.001 TRP H 35 HIS 0.003 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 3966) covalent geometry : angle 0.64630 ( 5402) SS BOND : bond 0.00414 ( 4) SS BOND : angle 1.03976 ( 8) hydrogen bonds : bond 0.03229 ( 95) hydrogen bonds : angle 7.22917 ( 270) link_NAG-ASN : bond 0.00267 ( 1) link_NAG-ASN : angle 0.77200 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.150 Fit side-chains REVERT: L 24 ARG cc_start: 0.6476 (mtp180) cc_final: 0.6234 (mtp-110) outliers start: 5 outliers final: 3 residues processed: 51 average time/residue: 0.0777 time to fit residues: 5.0309 Evaluate side-chains 46 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain L residue 132 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 32 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 42 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 28 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 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 = 0.4244 r_free = 0.4244 target = 0.189507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.155565 restraints weight = 4013.524| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.29 r_work: 0.3734 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 3971 Z= 0.155 Angle : 0.631 7.466 5413 Z= 0.318 Chirality : 0.044 0.148 611 Planarity : 0.006 0.056 683 Dihedral : 5.437 24.949 552 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.05 % Allowed : 15.72 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.42 (0.39), residues: 480 helix: -5.40 (0.28), residues: 6 sheet: -1.90 (0.35), residues: 212 loop : -1.13 (0.41), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 250 TYR 0.014 0.002 TYR I 249 PHE 0.029 0.002 PHE I 298 TRP 0.010 0.001 TRP H 35 HIS 0.003 0.000 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 3966) covalent geometry : angle 0.63018 ( 5402) SS BOND : bond 0.00370 ( 4) SS BOND : angle 0.93351 ( 8) hydrogen bonds : bond 0.03000 ( 95) hydrogen bonds : angle 6.82658 ( 270) link_NAG-ASN : bond 0.00300 ( 1) link_NAG-ASN : angle 0.70319 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.154 Fit side-chains REVERT: L 24 ARG cc_start: 0.6521 (mtp180) cc_final: 0.6235 (mtp-110) REVERT: I 273 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7681 (tt) outliers start: 9 outliers final: 6 residues processed: 51 average time/residue: 0.0809 time to fit residues: 5.1494 Evaluate side-chains 52 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 289 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 295 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 = 0.4207 r_free = 0.4207 target = 0.185456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.151289 restraints weight = 4063.384| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.30 r_work: 0.3679 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 3971 Z= 0.223 Angle : 0.684 6.403 5413 Z= 0.347 Chirality : 0.046 0.183 611 Planarity : 0.007 0.056 683 Dihedral : 5.667 25.796 552 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 2.05 % Allowed : 17.08 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.45 (0.40), residues: 480 helix: -5.44 (0.28), residues: 6 sheet: -1.93 (0.36), residues: 211 loop : -1.14 (0.41), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 250 TYR 0.016 0.002 TYR L 36 PHE 0.030 0.003 PHE I 298 TRP 0.012 0.002 TRP H 48 HIS 0.003 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00552 ( 3966) covalent geometry : angle 0.68369 ( 5402) SS BOND : bond 0.00461 ( 4) SS BOND : angle 1.04937 ( 8) hydrogen bonds : bond 0.03286 ( 95) hydrogen bonds : angle 6.86037 ( 270) link_NAG-ASN : bond 0.00344 ( 1) link_NAG-ASN : angle 0.62623 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.133 Fit side-chains REVERT: L 24 ARG cc_start: 0.6554 (mtp180) cc_final: 0.6231 (mtp-110) outliers start: 9 outliers final: 7 residues processed: 48 average time/residue: 0.0732 time to fit residues: 4.5247 Evaluate side-chains 48 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain I residue 289 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 9 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 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 = 0.4225 r_free = 0.4225 target = 0.187348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.153252 restraints weight = 4070.138| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.30 r_work: 0.3705 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 3971 Z= 0.175 Angle : 0.648 7.388 5413 Z= 0.326 Chirality : 0.045 0.173 611 Planarity : 0.006 0.055 683 Dihedral : 5.451 25.285 552 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.05 % Allowed : 17.54 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.35 (0.40), residues: 480 helix: -5.43 (0.28), residues: 6 sheet: -1.84 (0.36), residues: 212 loop : -1.09 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 250 TYR 0.015 0.002 TYR H 51 PHE 0.033 0.002 PHE I 298 TRP 0.014 0.001 TRP H 35 HIS 0.002 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 3966) covalent geometry : angle 0.64714 ( 5402) SS BOND : bond 0.00497 ( 4) SS BOND : angle 1.07520 ( 8) hydrogen bonds : bond 0.03082 ( 95) hydrogen bonds : angle 6.67022 ( 270) link_NAG-ASN : bond 0.00306 ( 1) link_NAG-ASN : angle 0.66080 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.156 Fit side-chains REVERT: L 24 ARG cc_start: 0.6506 (mtp180) cc_final: 0.6181 (mtp-110) REVERT: I 295 GLN cc_start: 0.7188 (pt0) cc_final: 0.6941 (pt0) REVERT: I 306 TRP cc_start: 0.7513 (m-90) cc_final: 0.7205 (m-90) outliers start: 9 outliers final: 7 residues processed: 49 average time/residue: 0.0767 time to fit residues: 4.7783 Evaluate side-chains 49 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain I residue 289 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 chunk 29 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 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 = 0.4227 r_free = 0.4227 target = 0.187605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.153879 restraints weight = 3975.223| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.28 r_work: 0.3718 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 3971 Z= 0.165 Angle : 0.633 6.583 5413 Z= 0.319 Chirality : 0.044 0.167 611 Planarity : 0.006 0.055 683 Dihedral : 5.303 24.955 552 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 2.51 % Allowed : 17.08 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.41), residues: 480 helix: -5.44 (0.28), residues: 6 sheet: -1.77 (0.36), residues: 212 loop : -1.00 (0.43), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 250 TYR 0.015 0.002 TYR I 249 PHE 0.035 0.002 PHE I 298 TRP 0.013 0.001 TRP H 35 HIS 0.002 0.000 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 3966) covalent geometry : angle 0.63248 ( 5402) SS BOND : bond 0.00465 ( 4) SS BOND : angle 0.99637 ( 8) hydrogen bonds : bond 0.03014 ( 95) hydrogen bonds : angle 6.50584 ( 270) link_NAG-ASN : bond 0.00304 ( 1) link_NAG-ASN : angle 0.67062 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.169 Fit side-chains REVERT: L 24 ARG cc_start: 0.6474 (mtp180) cc_final: 0.6137 (mtp-110) REVERT: I 295 GLN cc_start: 0.7154 (pt0) cc_final: 0.6939 (pt0) REVERT: I 306 TRP cc_start: 0.7377 (m-90) cc_final: 0.7164 (m-90) outliers start: 11 outliers final: 8 residues processed: 48 average time/residue: 0.0703 time to fit residues: 4.3192 Evaluate side-chains 50 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain I residue 289 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 0.0980 chunk 14 optimal weight: 0.0470 chunk 41 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 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 = 0.4220 r_free = 0.4220 target = 0.186601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.153770 restraints weight = 3981.703| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.19 r_work: 0.3753 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 3971 Z= 0.161 Angle : 0.641 8.951 5413 Z= 0.319 Chirality : 0.044 0.165 611 Planarity : 0.006 0.055 683 Dihedral : 5.297 25.021 552 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.82 % Allowed : 17.31 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.12 (0.41), residues: 480 helix: -5.46 (0.28), residues: 6 sheet: -1.69 (0.37), residues: 212 loop : -0.92 (0.43), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 250 TYR 0.015 0.002 TYR I 249 PHE 0.036 0.002 PHE I 298 TRP 0.012 0.001 TRP H 35 HIS 0.002 0.000 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 3966) covalent geometry : angle 0.64064 ( 5402) SS BOND : bond 0.00466 ( 4) SS BOND : angle 1.02163 ( 8) hydrogen bonds : bond 0.02925 ( 95) hydrogen bonds : angle 6.39329 ( 270) link_NAG-ASN : bond 0.00300 ( 1) link_NAG-ASN : angle 0.68463 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.179 Fit side-chains REVERT: L 24 ARG cc_start: 0.6562 (mtp180) cc_final: 0.6200 (mtp-110) REVERT: I 297 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6024 (pm20) REVERT: I 306 TRP cc_start: 0.7412 (m-90) cc_final: 0.7165 (m-90) outliers start: 8 outliers final: 7 residues processed: 48 average time/residue: 0.0866 time to fit residues: 5.1215 Evaluate side-chains 49 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 297 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 29 optimal weight: 0.1980 chunk 41 optimal weight: 0.0980 chunk 18 optimal weight: 3.9990 chunk 47 optimal weight: 0.0270 chunk 2 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 overall best weight: 0.2838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 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 = 0.4257 r_free = 0.4257 target = 0.190795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.157340 restraints weight = 3988.401| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.27 r_work: 0.3751 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3971 Z= 0.126 Angle : 0.612 7.324 5413 Z= 0.305 Chirality : 0.044 0.162 611 Planarity : 0.006 0.055 683 Dihedral : 5.116 25.894 552 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 1.82 % Allowed : 18.00 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.41), residues: 480 helix: -5.47 (0.28), residues: 6 sheet: -1.55 (0.37), residues: 213 loop : -0.81 (0.43), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 250 TYR 0.013 0.001 TYR I 249 PHE 0.034 0.002 PHE I 298 TRP 0.013 0.001 TRP H 35 HIS 0.002 0.000 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 3966) covalent geometry : angle 0.61133 ( 5402) SS BOND : bond 0.00436 ( 4) SS BOND : angle 0.96854 ( 8) hydrogen bonds : bond 0.02803 ( 95) hydrogen bonds : angle 6.16433 ( 270) link_NAG-ASN : bond 0.00256 ( 1) link_NAG-ASN : angle 0.72932 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.174 Fit side-chains REVERT: L 24 ARG cc_start: 0.6504 (mtp180) cc_final: 0.6119 (mtp-110) REVERT: I 306 TRP cc_start: 0.7228 (m-90) cc_final: 0.6938 (m-90) outliers start: 8 outliers final: 7 residues processed: 51 average time/residue: 0.0836 time to fit residues: 5.3483 Evaluate side-chains 49 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain I residue 289 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 275 HIS ** I 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.184147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.149871 restraints weight = 4023.998| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.29 r_work: 0.3670 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 3971 Z= 0.239 Angle : 0.711 7.949 5413 Z= 0.355 Chirality : 0.047 0.165 611 Planarity : 0.006 0.055 683 Dihedral : 5.467 27.241 552 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 2.28 % Allowed : 17.77 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.42), residues: 480 helix: -5.47 (0.27), residues: 6 sheet: -1.68 (0.37), residues: 212 loop : -0.91 (0.43), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 250 TYR 0.025 0.002 TYR L 87 PHE 0.040 0.003 PHE I 298 TRP 0.012 0.002 TRP H 35 HIS 0.004 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00581 ( 3966) covalent geometry : angle 0.70974 ( 5402) SS BOND : bond 0.00663 ( 4) SS BOND : angle 1.18076 ( 8) hydrogen bonds : bond 0.03203 ( 95) hydrogen bonds : angle 6.52173 ( 270) link_NAG-ASN : bond 0.00352 ( 1) link_NAG-ASN : angle 0.68738 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1209.47 seconds wall clock time: 21 minutes 30.40 seconds (1290.40 seconds total)