Starting phenix.real_space_refine on Tue Feb 3 13:13:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xzr_72369/02_2026/9xzr_72369_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xzr_72369/02_2026/9xzr_72369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xzr_72369/02_2026/9xzr_72369_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xzr_72369/02_2026/9xzr_72369_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xzr_72369/02_2026/9xzr_72369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xzr_72369/02_2026/9xzr_72369.map" } resolution = 3.37 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= 0.002 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 P 71 5.49 5 S 7 5.16 5 C 1602 2.51 5 N 521 2.21 5 O 780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2981 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1511 Classifications: {'RNA': 71} Modifications used: {'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 4, 'rna3p_pur': 27, 'rna3p_pyr': 33} Link IDs: {'rna2p': 11, 'rna3p': 59} Chain: "B" Number of atoms: 1442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1442 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 170} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'AN6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.60, per 1000 atoms: 0.20 Number of scatterers: 2981 At special positions: 0 Unit cell: (54.384, 65.92, 88.992, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 7 16.00 P 71 15.00 O 780 8.00 N 521 7.00 C 1602 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.17 Conformation dependent library (CDL) restraints added in 36.4 milliseconds 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 338 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 1 sheets defined 33.3% alpha, 7.9% beta 16 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'B' and resid 108 through 129 Processing helix chain 'B' and resid 144 through 151 removed outlier: 3.692A pdb=" N PHE B 148 " --> pdb=" O LEU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'B' and resid 216 through 225 Processing helix chain 'B' and resid 247 through 257 Processing sheet with id=AA1, first strand: chain 'B' and resid 163 through 165 removed outlier: 3.587A pdb=" N LYS B 164 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE B 97 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA B 138 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LEU B 99 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLU B 96 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL B 184 " --> pdb=" O ILE B 204 " (cutoff:3.500A) 37 hydrogen bonds defined for protein. 105 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 0.27 Time building geometry restraints manager: 0.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 369 1.32 - 1.44: 1236 1.44 - 1.56: 1424 1.56 - 1.69: 142 1.69 - 1.81: 13 Bond restraints: 3184 Sorted by residual: bond pdb=" C4' G A 9 " pdb=" C3' G A 9 " ideal model delta sigma weight residual 1.527 1.273 0.254 1.50e-02 4.44e+03 2.86e+02 bond pdb=" C4' G A 9 " pdb=" O4' G A 9 " ideal model delta sigma weight residual 1.454 1.693 -0.239 1.50e-02 4.44e+03 2.54e+02 bond pdb=" C2' AN6 A 101 " pdb=" C3' AN6 A 101 " ideal model delta sigma weight residual 1.532 1.292 0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C6 AN6 A 101 " pdb=" N6 AN6 A 101 " ideal model delta sigma weight residual 1.334 1.511 -0.177 2.00e-02 2.50e+03 7.79e+01 bond pdb=" C2' G A 9 " pdb=" O2' G A 9 " ideal model delta sigma weight residual 1.412 1.288 0.124 1.50e-02 4.44e+03 6.78e+01 ... (remaining 3179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.10: 4633 9.10 - 18.20: 10 18.20 - 27.29: 1 27.29 - 36.39: 0 36.39 - 45.49: 1 Bond angle restraints: 4645 Sorted by residual: angle pdb=" C3' G A 9 " pdb=" O3' G A 9 " pdb=" P G A 10 " ideal model delta sigma weight residual 120.20 165.69 -45.49 1.50e+00 4.44e-01 9.20e+02 angle pdb=" O3' C A 48 " pdb=" C3' C A 48 " pdb=" C2' C A 48 " ideal model delta sigma weight residual 113.70 131.71 -18.01 1.50e+00 4.44e-01 1.44e+02 angle pdb=" C4' C A 48 " pdb=" C3' C A 48 " pdb=" O3' C A 48 " ideal model delta sigma weight residual 113.00 97.49 15.51 1.50e+00 4.44e-01 1.07e+02 angle pdb=" O3' U A 8 " pdb=" P G A 9 " pdb=" OP1 G A 9 " ideal model delta sigma weight residual 108.00 85.32 22.68 3.00e+00 1.11e-01 5.71e+01 angle pdb=" O5' G A 9 " pdb=" C5' G A 9 " pdb=" C4' G A 9 " ideal model delta sigma weight residual 111.70 122.08 -10.38 1.50e+00 4.44e-01 4.79e+01 ... (remaining 4640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 1812 35.05 - 70.10: 194 70.10 - 105.15: 26 105.15 - 140.20: 0 140.20 - 175.25: 3 Dihedral angle restraints: 2035 sinusoidal: 1515 harmonic: 520 Sorted by residual: dihedral pdb=" O4' U A 8 " pdb=" C1' U A 8 " pdb=" N1 U A 8 " pdb=" C2 U A 8 " ideal model delta sinusoidal sigma weight residual -128.00 24.20 -152.20 1 1.70e+01 3.46e-03 6.26e+01 dihedral pdb=" O4' U A 13 " pdb=" C1' U A 13 " pdb=" N1 U A 13 " pdb=" C2 U A 13 " ideal model delta sinusoidal sigma weight residual -160.00 -75.01 -84.99 1 1.50e+01 4.44e-03 3.89e+01 dihedral pdb=" C3' G A 44 " pdb=" C4' G A 44 " pdb=" O4' G A 44 " pdb=" C1' G A 44 " ideal model delta sinusoidal sigma weight residual 20.00 -8.81 28.81 1 8.00e+00 1.56e-02 1.86e+01 ... (remaining 2032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 575 0.328 - 0.657: 1 0.657 - 0.985: 0 0.985 - 1.314: 0 1.314 - 1.642: 1 Chirality restraints: 577 Sorted by residual: chirality pdb=" P G A 9 " pdb=" OP1 G A 9 " pdb=" OP2 G A 9 " pdb=" O5' G A 9 " both_signs ideal model delta sigma weight residual True 2.41 -0.77 1.64 2.00e-01 2.50e+01 6.74e+01 chirality pdb=" C3' AN6 A 101 " pdb=" C2' AN6 A 101 " pdb=" C4' AN6 A 101 " pdb=" O3' AN6 A 101 " both_signs ideal model delta sigma weight residual False -2.72 -2.32 -0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CB ILE B 178 " pdb=" CA ILE B 178 " pdb=" CG1 ILE B 178 " pdb=" CG2 ILE B 178 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 574 not shown) Planarity restraints: 328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 114 " -0.019 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C SER B 114 " 0.064 2.00e-02 2.50e+03 pdb=" O SER B 114 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU B 115 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 63 " 0.004 2.00e-02 2.50e+03 1.95e-02 1.14e+01 pdb=" N9 G A 63 " 0.018 2.00e-02 2.50e+03 pdb=" C8 G A 63 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G A 63 " -0.004 2.00e-02 2.50e+03 pdb=" C5 G A 63 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G A 63 " 0.011 2.00e-02 2.50e+03 pdb=" O6 G A 63 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G A 63 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G A 63 " -0.054 2.00e-02 2.50e+03 pdb=" N2 G A 63 " 0.033 2.00e-02 2.50e+03 pdb=" N3 G A 63 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G A 63 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 41 " -0.019 2.00e-02 2.50e+03 1.97e-02 8.69e+00 pdb=" N1 U A 41 " 0.047 2.00e-02 2.50e+03 pdb=" C2 U A 41 " -0.028 2.00e-02 2.50e+03 pdb=" O2 U A 41 " 0.008 2.00e-02 2.50e+03 pdb=" N3 U A 41 " 0.004 2.00e-02 2.50e+03 pdb=" C4 U A 41 " -0.001 2.00e-02 2.50e+03 pdb=" O4 U A 41 " -0.000 2.00e-02 2.50e+03 pdb=" C5 U A 41 " -0.006 2.00e-02 2.50e+03 pdb=" C6 U A 41 " -0.004 2.00e-02 2.50e+03 ... (remaining 325 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 898 2.82 - 3.34: 2837 3.34 - 3.86: 5838 3.86 - 4.38: 6525 4.38 - 4.90: 9015 Nonbonded interactions: 25113 Sorted by model distance: nonbonded pdb=" N6 A A 20 " pdb=" N4 C A 46 " model vdw 2.299 3.200 nonbonded pdb=" OP2 G A 10 " pdb=" OG SER B 114 " model vdw 2.309 3.040 nonbonded pdb=" O2' C A 47 " pdb=" O4' C A 48 " model vdw 2.350 3.040 nonbonded pdb=" O2' A A 27 " pdb=" O4' A A 28 " model vdw 2.412 3.040 nonbonded pdb=" O2' AN6 A 101 " pdb=" O3' AN6 A 101 " model vdw 2.420 2.432 ... (remaining 25108 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.280 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 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 : 0.013 0.254 3185 Z= 0.726 Angle : 1.317 45.489 4645 Z= 0.749 Chirality : 0.089 1.642 577 Planarity : 0.005 0.038 328 Dihedral : 23.939 175.250 1697 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.92 % Favored : 89.08 % Rotamer: Outliers : 3.12 % Allowed : 20.62 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.65), residues: 174 helix: -0.87 (0.71), residues: 50 sheet: -2.21 (1.40), residues: 12 loop : -2.61 (0.64), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 128 TYR 0.009 0.001 TYR B 237 PHE 0.008 0.001 PHE B 132 TRP 0.006 0.002 TRP B 160 HIS 0.002 0.001 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.01267 ( 3184) covalent geometry : angle 1.31732 ( 4645) hydrogen bonds : bond 0.13704 ( 80) hydrogen bonds : angle 6.34816 ( 187) Misc. bond : bond 0.01354 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.073 Fit side-chains revert: symmetry clash REVERT: B 107 MET cc_start: 0.7863 (mpp) cc_final: 0.7492 (mmp) REVERT: B 115 LEU cc_start: 0.9065 (tp) cc_final: 0.8760 (tp) REVERT: B 124 SER cc_start: 0.9167 (p) cc_final: 0.8750 (t) REVERT: B 208 ILE cc_start: 0.5129 (OUTLIER) cc_final: 0.4804 (pt) REVERT: B 215 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.7978 (tppt) REVERT: B 253 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8304 (tm-30) REVERT: B 254 LEU cc_start: 0.9420 (mt) cc_final: 0.8835 (mt) REVERT: B 259 PHE cc_start: 0.8460 (p90) cc_final: 0.7506 (p90) outliers start: 5 outliers final: 0 residues processed: 33 average time/residue: 0.0672 time to fit residues: 2.6043 Evaluate side-chains 26 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 215 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 0.0770 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.0770 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.088559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.074687 restraints weight = 16531.080| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 4.70 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3185 Z= 0.126 Angle : 0.611 5.236 4645 Z= 0.308 Chirality : 0.038 0.261 577 Planarity : 0.004 0.040 328 Dihedral : 24.515 163.022 1330 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.88 % Allowed : 22.50 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -1.70 (0.70), residues: 174 helix: 1.32 (0.77), residues: 50 sheet: -1.86 (1.55), residues: 12 loop : -2.38 (0.65), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 121 TYR 0.003 0.001 TYR B 237 PHE 0.012 0.002 PHE B 259 TRP 0.001 0.000 TRP B 160 HIS 0.001 0.000 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 3184) covalent geometry : angle 0.61123 ( 4645) hydrogen bonds : bond 0.05678 ( 80) hydrogen bonds : angle 4.23084 ( 187) Misc. bond : bond 0.00105 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.044 Fit side-chains REVERT: B 107 MET cc_start: 0.7710 (mpp) cc_final: 0.6860 (mmt) REVERT: B 124 SER cc_start: 0.9314 (p) cc_final: 0.8986 (t) REVERT: B 215 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.7859 (tppp) REVERT: B 253 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8420 (tm-30) REVERT: B 254 LEU cc_start: 0.9477 (mt) cc_final: 0.8897 (mt) outliers start: 3 outliers final: 1 residues processed: 32 average time/residue: 0.0416 time to fit residues: 1.6415 Evaluate side-chains 26 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 215 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 5 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 20 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.073625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.057833 restraints weight = 14595.738| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 4.91 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3185 Z= 0.216 Angle : 0.700 5.083 4645 Z= 0.360 Chirality : 0.039 0.261 577 Planarity : 0.005 0.035 328 Dihedral : 24.594 171.114 1328 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.22 % Favored : 86.78 % Rotamer: Outliers : 7.50 % Allowed : 22.50 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.65), residues: 174 helix: 1.42 (0.72), residues: 49 sheet: -1.89 (1.50), residues: 12 loop : -2.86 (0.59), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 121 TYR 0.014 0.002 TYR B 123 PHE 0.026 0.003 PHE B 173 TRP 0.002 0.001 TRP B 160 HIS 0.006 0.002 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 3184) covalent geometry : angle 0.69998 ( 4645) hydrogen bonds : bond 0.06632 ( 80) hydrogen bonds : angle 4.37161 ( 187) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 27 time to evaluate : 0.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 98 ILE cc_start: 0.7250 (mt) cc_final: 0.7042 (mt) REVERT: B 107 MET cc_start: 0.7685 (mpp) cc_final: 0.6580 (mmt) REVERT: B 121 ARG cc_start: 0.9349 (OUTLIER) cc_final: 0.8892 (mtm-85) REVERT: B 124 SER cc_start: 0.9429 (p) cc_final: 0.9147 (t) REVERT: B 215 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.7991 (tppp) REVERT: B 253 GLN cc_start: 0.9127 (tm-30) cc_final: 0.8641 (tm-30) REVERT: B 254 LEU cc_start: 0.9558 (mt) cc_final: 0.9056 (mt) outliers start: 12 outliers final: 7 residues processed: 36 average time/residue: 0.0556 time to fit residues: 2.3639 Evaluate side-chains 33 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 251 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 0.2980 chunk 19 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 23 optimal weight: 0.0070 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 117 ASN ** 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 = 0.3912 r_free = 0.3912 target = 0.082207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.067727 restraints weight = 16916.189| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 4.90 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3185 Z= 0.126 Angle : 0.570 4.811 4645 Z= 0.298 Chirality : 0.036 0.247 577 Planarity : 0.004 0.035 328 Dihedral : 24.450 173.169 1328 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 5.62 % Allowed : 26.25 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -1.80 (0.66), residues: 174 helix: 1.54 (0.75), residues: 50 sheet: -1.42 (1.63), residues: 12 loop : -2.68 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 230 TYR 0.005 0.001 TYR B 203 PHE 0.013 0.002 PHE B 132 TRP 0.001 0.001 TRP B 160 HIS 0.005 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 3184) covalent geometry : angle 0.56998 ( 4645) hydrogen bonds : bond 0.04462 ( 80) hydrogen bonds : angle 4.10997 ( 187) Misc. bond : bond 0.00032 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 107 MET cc_start: 0.7686 (mpp) cc_final: 0.7414 (mmp) REVERT: B 124 SER cc_start: 0.9402 (p) cc_final: 0.9102 (t) REVERT: B 208 ILE cc_start: 0.5762 (OUTLIER) cc_final: 0.4231 (pt) REVERT: B 215 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8068 (tptm) REVERT: B 253 GLN cc_start: 0.9051 (tm-30) cc_final: 0.8543 (tm-30) REVERT: B 254 LEU cc_start: 0.9541 (mt) cc_final: 0.8978 (mt) outliers start: 9 outliers final: 5 residues processed: 34 average time/residue: 0.0689 time to fit residues: 2.7725 Evaluate side-chains 32 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 215 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 117 ASN ** 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 = 0.3803 r_free = 0.3803 target = 0.072684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.057029 restraints weight = 14312.705| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 4.76 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3185 Z= 0.149 Angle : 0.595 7.323 4645 Z= 0.311 Chirality : 0.036 0.269 577 Planarity : 0.004 0.033 328 Dihedral : 24.607 175.476 1328 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.64 % Favored : 87.36 % Rotamer: Outliers : 6.25 % Allowed : 28.12 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -1.97 (0.65), residues: 174 helix: 1.52 (0.75), residues: 50 sheet: -1.62 (1.49), residues: 12 loop : -2.84 (0.57), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 127 TYR 0.007 0.001 TYR B 203 PHE 0.014 0.002 PHE B 173 TRP 0.001 0.000 TRP B 160 HIS 0.002 0.001 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3184) covalent geometry : angle 0.59504 ( 4645) hydrogen bonds : bond 0.04855 ( 80) hydrogen bonds : angle 4.18710 ( 187) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.044 Fit side-chains revert: symmetry clash REVERT: B 107 MET cc_start: 0.7791 (mpp) cc_final: 0.7365 (mmp) REVERT: B 124 SER cc_start: 0.9381 (p) cc_final: 0.9082 (t) REVERT: B 208 ILE cc_start: 0.5949 (OUTLIER) cc_final: 0.4970 (pt) REVERT: B 215 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8221 (tptm) REVERT: B 230 ARG cc_start: 0.8912 (mmt90) cc_final: 0.8666 (mmt-90) REVERT: B 253 GLN cc_start: 0.9077 (tm-30) cc_final: 0.8589 (tm-30) REVERT: B 254 LEU cc_start: 0.9551 (mt) cc_final: 0.9005 (mt) outliers start: 10 outliers final: 5 residues processed: 33 average time/residue: 0.0533 time to fit residues: 2.1317 Evaluate side-chains 34 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 245 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 117 ASN ** 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 = 0.3884 r_free = 0.3884 target = 0.079734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.064986 restraints weight = 16590.920| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 4.67 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3185 Z= 0.150 Angle : 0.594 7.392 4645 Z= 0.308 Chirality : 0.036 0.260 577 Planarity : 0.004 0.034 328 Dihedral : 24.643 173.730 1328 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 7.50 % Allowed : 26.88 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.64), residues: 174 helix: 1.44 (0.75), residues: 50 sheet: -1.56 (1.48), residues: 12 loop : -2.85 (0.55), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 202 TYR 0.005 0.001 TYR B 203 PHE 0.007 0.002 PHE B 132 TRP 0.002 0.001 TRP B 160 HIS 0.001 0.001 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 3184) covalent geometry : angle 0.59435 ( 4645) hydrogen bonds : bond 0.04883 ( 80) hydrogen bonds : angle 4.06335 ( 187) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 27 time to evaluate : 0.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.8157 (m-30) cc_final: 0.7956 (m-30) REVERT: B 107 MET cc_start: 0.7789 (mpp) cc_final: 0.6775 (mmp) REVERT: B 108 ASN cc_start: 0.8076 (OUTLIER) cc_final: 0.7640 (m-40) REVERT: B 124 SER cc_start: 0.9381 (p) cc_final: 0.9067 (t) REVERT: B 253 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8547 (tm-30) REVERT: B 254 LEU cc_start: 0.9549 (mt) cc_final: 0.8985 (mt) outliers start: 12 outliers final: 6 residues processed: 36 average time/residue: 0.0734 time to fit residues: 3.1248 Evaluate side-chains 32 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 215 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.081171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.066114 restraints weight = 16637.507| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 4.69 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3185 Z= 0.128 Angle : 0.626 8.204 4645 Z= 0.326 Chirality : 0.037 0.261 577 Planarity : 0.004 0.033 328 Dihedral : 24.608 173.994 1328 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 5.62 % Allowed : 32.50 % Favored : 61.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.63), residues: 174 helix: 1.27 (0.74), residues: 50 sheet: -1.50 (1.57), residues: 12 loop : -2.75 (0.55), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 244 TYR 0.004 0.001 TYR B 203 PHE 0.008 0.002 PHE B 259 TRP 0.001 0.000 TRP B 160 HIS 0.001 0.000 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 3184) covalent geometry : angle 0.62560 ( 4645) hydrogen bonds : bond 0.04709 ( 80) hydrogen bonds : angle 4.02917 ( 187) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.8277 (m-30) cc_final: 0.8056 (m-30) REVERT: B 107 MET cc_start: 0.7747 (mpp) cc_final: 0.6691 (mmp) REVERT: B 121 ARG cc_start: 0.9295 (OUTLIER) cc_final: 0.9005 (mtt-85) REVERT: B 124 SER cc_start: 0.9343 (p) cc_final: 0.9048 (t) REVERT: B 253 GLN cc_start: 0.9040 (tm-30) cc_final: 0.8534 (tm-30) REVERT: B 254 LEU cc_start: 0.9545 (mt) cc_final: 0.8984 (mt) outliers start: 9 outliers final: 7 residues processed: 35 average time/residue: 0.0498 time to fit residues: 2.0691 Evaluate side-chains 34 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 250 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 117 ASN ** 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 = 0.3814 r_free = 0.3814 target = 0.076122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.060910 restraints weight = 17410.040| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 4.86 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3185 Z= 0.230 Angle : 0.719 7.501 4645 Z= 0.372 Chirality : 0.040 0.276 577 Planarity : 0.005 0.036 328 Dihedral : 25.002 178.238 1328 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.79 % Favored : 86.21 % Rotamer: Outliers : 6.25 % Allowed : 33.12 % Favored : 60.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.63), residues: 174 helix: 0.40 (0.72), residues: 56 sheet: -2.83 (1.14), residues: 23 loop : -2.59 (0.59), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 244 TYR 0.008 0.002 TYR B 123 PHE 0.018 0.003 PHE B 173 TRP 0.003 0.001 TRP B 160 HIS 0.003 0.001 HIS B 262 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 3184) covalent geometry : angle 0.71938 ( 4645) hydrogen bonds : bond 0.07064 ( 80) hydrogen bonds : angle 4.33942 ( 187) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 MET cc_start: 0.8014 (mpp) cc_final: 0.6780 (mmt) REVERT: B 108 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7687 (m-40) REVERT: B 124 SER cc_start: 0.9355 (p) cc_final: 0.9081 (t) REVERT: B 225 MET cc_start: 0.8387 (mmp) cc_final: 0.8150 (mmp) REVERT: B 230 ARG cc_start: 0.8927 (mmt90) cc_final: 0.8580 (mmt-90) REVERT: B 253 GLN cc_start: 0.8946 (tm-30) cc_final: 0.8399 (tm-30) REVERT: B 254 LEU cc_start: 0.9508 (mt) cc_final: 0.8966 (mt) outliers start: 10 outliers final: 7 residues processed: 32 average time/residue: 0.0604 time to fit residues: 2.2473 Evaluate side-chains 32 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 245 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.0570 chunk 3 optimal weight: 10.0000 chunk 14 optimal weight: 0.0270 chunk 1 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN B 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.073728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.058146 restraints weight = 14009.849| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 4.52 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3185 Z= 0.123 Angle : 0.628 7.690 4645 Z= 0.329 Chirality : 0.037 0.279 577 Planarity : 0.004 0.035 328 Dihedral : 24.745 176.684 1328 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 3.75 % Allowed : 33.75 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.63), residues: 174 helix: 0.97 (0.72), residues: 50 sheet: -2.73 (1.23), residues: 22 loop : -2.58 (0.58), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 202 TYR 0.003 0.001 TYR B 185 PHE 0.007 0.001 PHE B 259 TRP 0.004 0.001 TRP B 160 HIS 0.002 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 3184) covalent geometry : angle 0.62824 ( 4645) hydrogen bonds : bond 0.04885 ( 80) hydrogen bonds : angle 3.89707 ( 187) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.047 Fit side-chains REVERT: B 108 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7725 (m-40) REVERT: B 121 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.8776 (mtt-85) REVERT: B 124 SER cc_start: 0.9293 (p) cc_final: 0.9003 (t) REVERT: B 208 ILE cc_start: 0.5360 (OUTLIER) cc_final: 0.4996 (pp) REVERT: B 215 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8560 (tppt) REVERT: B 230 ARG cc_start: 0.8968 (mmt90) cc_final: 0.8688 (mmt-90) REVERT: B 253 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8530 (tm-30) REVERT: B 254 LEU cc_start: 0.9572 (mt) cc_final: 0.9010 (mt) outliers start: 6 outliers final: 2 residues processed: 34 average time/residue: 0.0639 time to fit residues: 2.5854 Evaluate side-chains 32 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 215 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 5 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.071573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.055946 restraints weight = 14000.542| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 4.52 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.5795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3185 Z= 0.166 Angle : 0.631 7.721 4645 Z= 0.329 Chirality : 0.037 0.276 577 Planarity : 0.005 0.039 328 Dihedral : 24.818 179.875 1328 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 4.38 % Allowed : 31.25 % Favored : 64.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.64), residues: 174 helix: 0.65 (0.73), residues: 56 sheet: -2.75 (1.22), residues: 22 loop : -2.43 (0.60), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 127 TYR 0.006 0.001 TYR B 123 PHE 0.008 0.002 PHE B 132 TRP 0.001 0.000 TRP B 160 HIS 0.002 0.001 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 3184) covalent geometry : angle 0.63092 ( 4645) hydrogen bonds : bond 0.05427 ( 80) hydrogen bonds : angle 3.97454 ( 187) Misc. bond : bond 0.00028 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.077 Fit side-chains revert: symmetry clash REVERT: B 124 SER cc_start: 0.9343 (p) cc_final: 0.9039 (t) REVERT: B 208 ILE cc_start: 0.5314 (OUTLIER) cc_final: 0.4824 (pp) REVERT: B 230 ARG cc_start: 0.8994 (mmt90) cc_final: 0.8720 (mmt-90) REVERT: B 253 GLN cc_start: 0.9088 (tm-30) cc_final: 0.8576 (tm-30) REVERT: B 254 LEU cc_start: 0.9551 (mt) cc_final: 0.9037 (mt) outliers start: 7 outliers final: 5 residues processed: 31 average time/residue: 0.0620 time to fit residues: 2.3123 Evaluate side-chains 30 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 218 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 117 ASN ** 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 = 0.3766 r_free = 0.3766 target = 0.073516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.058525 restraints weight = 17368.291| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 4.66 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.6647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 3185 Z= 0.304 Angle : 0.783 7.274 4645 Z= 0.403 Chirality : 0.042 0.256 577 Planarity : 0.006 0.032 328 Dihedral : 25.148 173.497 1328 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 24.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.79 % Favored : 86.21 % Rotamer: Outliers : 5.00 % Allowed : 31.88 % Favored : 63.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.64), residues: 174 helix: 0.23 (0.70), residues: 57 sheet: -3.21 (1.11), residues: 23 loop : -2.53 (0.62), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 230 TYR 0.010 0.002 TYR B 185 PHE 0.012 0.003 PHE B 140 TRP 0.006 0.002 TRP B 160 HIS 0.003 0.001 HIS B 262 Details of bonding type rmsd covalent geometry : bond 0.00605 ( 3184) covalent geometry : angle 0.78281 ( 4645) hydrogen bonds : bond 0.07957 ( 80) hydrogen bonds : angle 4.36411 ( 187) Misc. bond : bond 0.00072 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 652.15 seconds wall clock time: 11 minutes 54.10 seconds (714.10 seconds total)