Starting phenix.real_space_refine on Wed Jul 1 21:36:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xzr_72369/07_2026/9xzr_72369_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xzr_72369/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9xzr_72369/07_2026/9xzr_72369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xzr_72369/07_2026/9xzr_72369.map" model { file = "/net/cci-nas-00/data/ceres_data/9xzr_72369/07_2026/9xzr_72369_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xzr_72369/07_2026/9xzr_72369_neut.cif" } 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-dev-6108/lib/python3.11/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: 0.92, per 1000 atoms: 0.31 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: 0.36 Conformation dependent library (CDL) restraints added in 62.4 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: 0.40 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: 0.46 Time building geometry restraints manager: 0.37 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=" N3 G A 9 " pdb=" C4 G A 9 " ideal model delta sigma weight residual 1.350 1.473 -0.123 7.00e-03 2.04e+04 3.07e+02 bond pdb=" C2 G A 9 " pdb=" N3 G A 9 " ideal model delta sigma weight residual 1.323 1.459 -0.136 8.00e-03 1.56e+04 2.87e+02 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=" C5 G A 9 " pdb=" C6 G A 9 " ideal model delta sigma weight residual 1.419 1.543 -0.124 1.00e-02 1.00e+04 1.53e+02 ... (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=" C5 G A 9 " pdb=" C4 G A 9 " pdb=" N3 G A 9 " ideal model delta sigma weight residual 128.60 119.71 8.89 5.00e-01 4.00e+00 3.16e+02 angle pdb=" C5 G A 9 " pdb=" C6 G A 9 " pdb=" N1 G A 9 " ideal model delta sigma weight residual 111.50 119.73 -8.23 5.00e-01 4.00e+00 2.71e+02 angle pdb=" C2 G A 9 " pdb=" N3 G A 9 " pdb=" C4 G A 9 " ideal model delta sigma weight residual 111.90 119.75 -7.85 5.00e-01 4.00e+00 2.47e+02 angle pdb=" C5 G A 9 " pdb=" C6 G A 9 " pdb=" O6 G A 9 " ideal model delta sigma weight residual 128.60 119.43 9.17 6.00e-01 2.78e+00 2.34e+02 ... (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: 1.160 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.780 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 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= 0.920 Angle : 1.317 45.489 4645 Z= 1.035 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/Z covalent geometry : bond 0.01267 / 0.92 ( 3184) covalent geometry : angle 1.31736 / 1.03 ( 4645) hydrogen bonds : bond 0.13704 / 14.36 ( 80) hydrogen bonds : angle 6.34816 / 7.79 ( 187) Misc. bond : bond 0.01354 / 0.68 ( 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 : 0.076 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: 0.0837 time to fit residues: 3.2369 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 : 0.049 ------------------------------------------------------------------------------- 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: 3.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.0770 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.090010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.075941 restraints weight = 16415.971| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 4.83 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3185 Z= 0.136 Angle : 0.578 5.824 4645 Z= 0.338 Chirality : 0.041 0.256 577 Planarity : 0.004 0.038 328 Dihedral : 24.853 167.247 1330 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % 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: -2.05 (0.68), residues: 174 helix: 0.91 (0.74), residues: 50 sheet: -2.06 (1.50), residues: 12 loop : -2.54 (0.64), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 230 TYR 0.006 0.001 TYR B 214 PHE 0.021 0.002 PHE B 259 TRP 0.001 0.000 TRP B 160 HIS 0.004 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 ( 3184) covalent geometry : angle 0.57845 / 0.34 ( 4645) hydrogen bonds : bond 0.08104 / 7.67 ( 80) hydrogen bonds : angle 4.70727 / 5.83 ( 187) Misc. bond : bond 0.00115 / 0.06 ( 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 31 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: B 107 MET cc_start: 0.7557 (mpp) cc_final: 0.7330 (mmp) REVERT: B 124 SER cc_start: 0.9307 (p) cc_final: 0.8924 (t) REVERT: B 208 ILE cc_start: 0.5111 (OUTLIER) cc_final: 0.4555 (pt) REVERT: B 215 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.7885 (tppp) REVERT: B 253 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8518 (tm-30) REVERT: B 254 LEU cc_start: 0.9534 (mt) cc_final: 0.8991 (mt) outliers start: 3 outliers final: 1 residues processed: 31 average time/residue: 0.0671 time to fit residues: 2.5558 Evaluate side-chains 27 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 208 ILE 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: 1.9990 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3932 r_free = 0.3932 target = 0.084591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.070563 restraints weight = 16902.899| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 4.80 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3185 Z= 0.203 Angle : 0.559 5.149 4645 Z= 0.333 Chirality : 0.039 0.208 577 Planarity : 0.005 0.045 328 Dihedral : 24.831 163.932 1330 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.92 % Favored : 89.08 % Rotamer: Outliers : 4.38 % Allowed : 23.75 % Favored : 71.88 % 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: -1.92 (0.68), residues: 174 helix: 1.36 (0.76), residues: 50 sheet: -2.00 (1.45), residues: 12 loop : -2.65 (0.62), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 128 TYR 0.014 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 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.20 ( 3184) covalent geometry : angle 0.55914 / 0.33 ( 4645) hydrogen bonds : bond 0.07165 / 7.14 ( 80) hydrogen bonds : angle 4.66988 / 5.65 ( 187) Misc. bond : bond 0.00363 / 0.18 ( 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 31 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 107 MET cc_start: 0.7662 (mpp) cc_final: 0.7411 (mmp) REVERT: B 124 SER cc_start: 0.9436 (p) cc_final: 0.9132 (t) REVERT: B 208 ILE cc_start: 0.5937 (OUTLIER) cc_final: 0.5246 (pt) REVERT: B 215 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.7894 (tppp) REVERT: B 253 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8540 (tm-30) REVERT: B 254 LEU cc_start: 0.9562 (mt) cc_final: 0.9051 (mt) outliers start: 7 outliers final: 3 residues processed: 29 average time/residue: 0.0720 time to fit residues: 2.5621 Evaluate side-chains 30 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ASN 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: 10.0000 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 8 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.087023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.072735 restraints weight = 16579.604| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 4.85 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3185 Z= 0.113 Angle : 0.517 8.362 4645 Z= 0.292 Chirality : 0.038 0.258 577 Planarity : 0.004 0.039 328 Dihedral : 24.662 166.235 1330 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.50 % Allowed : 24.38 % Favored : 73.12 % 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: -1.77 (0.67), residues: 174 helix: 1.36 (0.78), residues: 50 sheet: -1.72 (1.55), residues: 12 loop : -2.50 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 243 TYR 0.005 0.001 TYR B 203 PHE 0.007 0.001 PHE B 259 TRP 0.003 0.001 TRP B 160 HIS 0.002 0.001 HIS B 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 ( 3184) covalent geometry : angle 0.51708 / 0.29 ( 4645) hydrogen bonds : bond 0.06393 / 5.91 ( 80) hydrogen bonds : angle 4.27501 / 5.17 ( 187) Misc. bond : bond 0.00131 / 0.07 ( 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 31 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 124 SER cc_start: 0.9355 (p) cc_final: 0.9014 (t) REVERT: B 208 ILE cc_start: 0.5697 (OUTLIER) cc_final: 0.5011 (pt) REVERT: B 215 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8028 (tppp) REVERT: B 253 GLN cc_start: 0.9036 (tm-30) cc_final: 0.8516 (tm-30) REVERT: B 254 LEU cc_start: 0.9536 (mt) cc_final: 0.8964 (mt) outliers start: 4 outliers final: 1 residues processed: 31 average time/residue: 0.0686 time to fit residues: 2.6008 Evaluate side-chains 28 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ASN 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: 0.7980 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 5 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3880 r_free = 0.3880 target = 0.076851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.061353 restraints weight = 14322.367| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 4.78 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3185 Z= 0.150 Angle : 0.507 5.842 4645 Z= 0.294 Chirality : 0.037 0.193 577 Planarity : 0.004 0.038 328 Dihedral : 24.572 172.258 1330 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.92 % Favored : 89.08 % Rotamer: Outliers : 3.75 % Allowed : 26.88 % Favored : 69.38 % 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: -1.81 (0.67), residues: 174 helix: 1.41 (0.77), residues: 50 sheet: -1.76 (1.49), residues: 12 loop : -2.57 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 128 TYR 0.010 0.001 TYR B 123 PHE 0.009 0.002 PHE B 259 TRP 0.002 0.001 TRP B 160 HIS 0.002 0.001 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 ( 3184) covalent geometry : angle 0.50651 / 0.29 ( 4645) hydrogen bonds : bond 0.06024 / 5.79 ( 80) hydrogen bonds : angle 4.30600 / 5.17 ( 187) Misc. bond : bond 0.00105 / 0.05 ( 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 31 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 121 ARG cc_start: 0.9382 (OUTLIER) cc_final: 0.9052 (mtm-85) REVERT: B 124 SER cc_start: 0.9416 (p) cc_final: 0.9124 (t) REVERT: B 208 ILE cc_start: 0.5215 (OUTLIER) cc_final: 0.4858 (pt) REVERT: B 215 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.7997 (tppp) REVERT: B 253 GLN cc_start: 0.9092 (tm-30) cc_final: 0.8591 (tm-30) REVERT: B 254 LEU cc_start: 0.9563 (mt) cc_final: 0.9042 (mt) outliers start: 6 outliers final: 2 residues processed: 30 average time/residue: 0.0595 time to fit residues: 2.0933 Evaluate side-chains 30 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.047 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 21 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3868 r_free = 0.3868 target = 0.076061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.060576 restraints weight = 14368.765| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 4.88 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3185 Z= 0.138 Angle : 0.528 7.585 4645 Z= 0.296 Chirality : 0.038 0.237 577 Planarity : 0.004 0.037 328 Dihedral : 24.541 175.690 1330 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 3.75 % Allowed : 26.88 % Favored : 69.38 % 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: -1.90 (0.66), residues: 174 helix: 1.38 (0.77), residues: 50 sheet: -1.73 (1.50), residues: 12 loop : -2.66 (0.58), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 230 TYR 0.008 0.001 TYR B 123 PHE 0.012 0.002 PHE B 165 TRP 0.002 0.001 TRP B 160 HIS 0.005 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 ( 3184) covalent geometry : angle 0.52825 / 0.30 ( 4645) hydrogen bonds : bond 0.05694 / 5.38 ( 80) hydrogen bonds : angle 4.22994 / 5.08 ( 187) Misc. bond : bond 0.00025 / 0.01 ( 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 33 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 121 ARG cc_start: 0.9389 (OUTLIER) cc_final: 0.8939 (mtt90) REVERT: B 124 SER cc_start: 0.9393 (p) cc_final: 0.9115 (t) REVERT: B 208 ILE cc_start: 0.5202 (OUTLIER) cc_final: 0.4822 (pt) REVERT: B 215 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.7970 (tppp) REVERT: B 253 GLN cc_start: 0.9111 (tm-30) cc_final: 0.8593 (tm-30) REVERT: B 254 LEU cc_start: 0.9562 (mt) cc_final: 0.9051 (mt) outliers start: 6 outliers final: 2 residues processed: 32 average time/residue: 0.0757 time to fit residues: 2.9024 Evaluate side-chains 30 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.075 ------------------------------------------------------------------------------- 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 208 ILE Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 245 VAL 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: 0.7980 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3923 r_free = 0.3923 target = 0.083131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.068901 restraints weight = 17126.942| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 4.84 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3185 Z= 0.114 Angle : 0.540 9.892 4645 Z= 0.292 Chirality : 0.037 0.237 577 Planarity : 0.004 0.035 328 Dihedral : 24.500 176.471 1330 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 3.75 % Allowed : 30.00 % Favored : 66.25 % 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: -1.87 (0.65), residues: 174 helix: 1.40 (0.77), residues: 50 sheet: -1.62 (1.51), residues: 12 loop : -2.65 (0.57), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 230 TYR 0.004 0.001 TYR B 123 PHE 0.009 0.002 PHE B 259 TRP 0.001 0.000 TRP B 160 HIS 0.003 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 ( 3184) covalent geometry : angle 0.54038 / 0.29 ( 4645) hydrogen bonds : bond 0.05336 / 4.85 ( 80) hydrogen bonds : angle 4.20359 / 4.96 ( 187) Misc. bond : bond 0.00023 / 0.01 ( 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 33 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 121 ARG cc_start: 0.9414 (OUTLIER) cc_final: 0.8933 (mtt90) REVERT: B 124 SER cc_start: 0.9419 (p) cc_final: 0.9145 (t) REVERT: B 208 ILE cc_start: 0.5423 (OUTLIER) cc_final: 0.5143 (pp) REVERT: B 215 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.7982 (tptm) REVERT: B 253 GLN cc_start: 0.9049 (tm-30) cc_final: 0.8500 (tm-30) REVERT: B 254 LEU cc_start: 0.9527 (mt) cc_final: 0.8965 (mt) outliers start: 6 outliers final: 2 residues processed: 32 average time/residue: 0.0940 time to fit residues: 3.5246 Evaluate side-chains 30 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.090 ------------------------------------------------------------------------------- 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 208 ILE Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 245 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 10 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3818 r_free = 0.3818 target = 0.073141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.057787 restraints weight = 14815.692| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 4.78 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3185 Z= 0.182 Angle : 0.588 7.131 4645 Z= 0.324 Chirality : 0.038 0.261 577 Planarity : 0.005 0.036 328 Dihedral : 24.644 179.461 1330 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 3.75 % Allowed : 30.00 % Favored : 66.25 % 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: -2.30 (0.64), residues: 174 helix: 1.38 (0.77), residues: 49 sheet: -2.54 (1.10), residues: 22 loop : -2.95 (0.57), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 230 TYR 0.015 0.002 TYR B 123 PHE 0.011 0.002 PHE B 140 TRP 0.002 0.001 TRP B 160 HIS 0.003 0.001 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.18 ( 3184) covalent geometry : angle 0.58753 / 0.32 ( 4645) hydrogen bonds : bond 0.06218 / 6.32 ( 80) hydrogen bonds : angle 4.32524 / 5.16 ( 187) Misc. bond : bond 0.00067 / 0.03 ( 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 32 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 ARG cc_start: 0.9387 (OUTLIER) cc_final: 0.9015 (mtm-85) REVERT: B 124 SER cc_start: 0.9457 (p) cc_final: 0.9191 (t) REVERT: B 208 ILE cc_start: 0.5579 (OUTLIER) cc_final: 0.5205 (pp) REVERT: B 253 GLN cc_start: 0.9133 (tm-30) cc_final: 0.8629 (tm-30) REVERT: B 254 LEU cc_start: 0.9558 (mt) cc_final: 0.9070 (mt) outliers start: 6 outliers final: 4 residues processed: 31 average time/residue: 0.0524 time to fit residues: 1.9146 Evaluate side-chains 31 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 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 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 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: 2.9990 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 14 optimal weight: 0.3980 chunk 1 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3837 r_free = 0.3837 target = 0.074643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.059175 restraints weight = 14567.031| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 4.88 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3786 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= 0.108 Angle : 0.524 7.275 4645 Z= 0.291 Chirality : 0.037 0.264 577 Planarity : 0.004 0.036 328 Dihedral : 24.631 176.053 1330 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 3.12 % Allowed : 30.62 % Favored : 66.25 % 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: -2.18 (0.64), residues: 174 helix: 1.28 (0.76), residues: 50 sheet: -2.31 (1.12), residues: 22 loop : -2.84 (0.57), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 230 TYR 0.004 0.001 TYR B 203 PHE 0.010 0.002 PHE B 259 TRP 0.002 0.000 TRP B 160 HIS 0.001 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.11 ( 3184) covalent geometry : angle 0.52402 / 0.29 ( 4645) hydrogen bonds : bond 0.05138 / 4.49 ( 80) hydrogen bonds : angle 4.10052 / 4.83 ( 187) Misc. bond : bond 0.00011 / 0.01 ( 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 32 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 SER cc_start: 0.9400 (p) cc_final: 0.9096 (t) REVERT: B 230 ARG cc_start: 0.8970 (mmt90) cc_final: 0.8658 (mmt-90) REVERT: B 253 GLN cc_start: 0.9130 (tm-30) cc_final: 0.8599 (tm-30) REVERT: B 254 LEU cc_start: 0.9550 (mt) cc_final: 0.9034 (mt) outliers start: 5 outliers final: 4 residues processed: 31 average time/residue: 0.0554 time to fit residues: 2.0157 Evaluate side-chains 30 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.045 ------------------------------------------------------------------------------- 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 215 LYS Chi-restraints excluded: chain B residue 245 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 21 optimal weight: 0.0770 chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.4980 chunk 5 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 overall best weight: 1.7144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3809 r_free = 0.3809 target = 0.072827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.057469 restraints weight = 14623.048| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 4.78 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3185 Z= 0.158 Angle : 0.574 8.117 4645 Z= 0.314 Chirality : 0.037 0.262 577 Planarity : 0.004 0.033 328 Dihedral : 24.647 178.665 1328 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 3.75 % Allowed : 30.00 % Favored : 66.25 % 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: -2.18 (0.64), residues: 174 helix: 1.41 (0.76), residues: 50 sheet: -2.33 (1.14), residues: 22 loop : -2.92 (0.57), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 244 TYR 0.010 0.001 TYR B 123 PHE 0.008 0.002 PHE B 259 TRP 0.002 0.001 TRP B 160 HIS 0.003 0.001 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 ( 3184) covalent geometry : angle 0.57442 / 0.31 ( 4645) hydrogen bonds : bond 0.05511 / 5.29 ( 80) hydrogen bonds : angle 4.10318 / 4.81 ( 187) Misc. bond : bond 0.00021 / 0.01 ( 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 31 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 ARG cc_start: 0.9414 (OUTLIER) cc_final: 0.9028 (mtm-85) REVERT: B 124 SER cc_start: 0.9441 (p) cc_final: 0.9172 (t) REVERT: B 253 GLN cc_start: 0.9108 (tm-30) cc_final: 0.8581 (tm-30) REVERT: B 254 LEU cc_start: 0.9534 (mt) cc_final: 0.9009 (mt) outliers start: 6 outliers final: 4 residues processed: 30 average time/residue: 0.0594 time to fit residues: 2.1293 Evaluate side-chains 30 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.045 ------------------------------------------------------------------------------- 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 159 ASN Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 245 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 10.9990 chunk 0 optimal weight: 20.0000 chunk 9 optimal weight: 0.7980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3768 r_free = 0.3768 target = 0.070679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.055205 restraints weight = 14751.100| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 4.80 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3185 Z= 0.247 Angle : 0.663 8.688 4645 Z= 0.364 Chirality : 0.040 0.283 577 Planarity : 0.005 0.030 328 Dihedral : 24.900 179.889 1328 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 24.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.37 % Favored : 85.63 % Rotamer: Outliers : 3.12 % Allowed : 30.62 % Favored : 66.25 % 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: -2.58 (0.64), residues: 174 helix: 0.53 (0.71), residues: 57 sheet: -3.72 (1.07), residues: 22 loop : -2.75 (0.60), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 213 TYR 0.018 0.002 TYR B 123 PHE 0.014 0.003 PHE B 173 TRP 0.003 0.001 TRP B 160 HIS 0.006 0.002 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.25 ( 3184) covalent geometry : angle 0.66341 / 0.36 ( 4645) hydrogen bonds : bond 0.07286 / 7.54 ( 80) hydrogen bonds : angle 4.34016 / 5.14 ( 187) Misc. bond : bond 0.00086 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 709.56 seconds wall clock time: 12 minutes 51.47 seconds (771.47 seconds total)