Starting phenix.real_space_refine on Tue Aug 4 12:44:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xzr_72369/08_2026/9xzr_72369_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xzr_72369/08_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_72369/08_2026/9xzr_72369_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xzr_72369/08_2026/9xzr_72369_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xzr_72369/08_2026/9xzr_72369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xzr_72369/08_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-2.2rc3-6140/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: 0.84, per 1000 atoms: 0.28 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: 0.18 Conformation dependent library (CDL) restraints added in 36.7 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: 0.29 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: 0.28 Time building geometry restraints manager: 0.24 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=" O4' G A 9 " ideal model delta sigma weight residual 1.454 1.693 -0.239 1.00e-02 1.00e+04 5.73e+02 bond pdb=" C4' G A 9 " pdb=" C3' G A 9 " ideal model delta sigma weight residual 1.527 1.273 0.254 1.10e-02 8.26e+03 5.32e+02 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=" 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 - 9.20: 4635 9.20 - 18.40: 8 18.40 - 27.59: 1 27.59 - 36.79: 0 36.79 - 45.99: 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 119.70 165.69 -45.99 1.20e+00 6.94e-01 1.47e+03 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=" O5' G A 9 " pdb=" C5' G A 9 " pdb=" C4' G A 9 " ideal model delta sigma weight residual 109.40 122.08 -12.68 8.00e-01 1.56e+00 2.51e+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 ... (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: 0.580 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: 0.010 Process input model: 3.790 Find NCS groups from input model: 0.000 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:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.340 ------------------------------------------------------------------------------- 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= 1.045 Angle : 1.389 45.989 4645 Z= 1.168 Chirality : 0.096 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 0.01272 / 1.04 ( 3184) covalent geometry : angle 1.38892 / 1.17 ( 4645) hydrogen bonds : bond 0.13704 / 15.85 ( 80) hydrogen bonds : angle 6.34816 / 8.24 ( 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 : 0.047 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: 0.0597 time to fit residues: 2.2917 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: 6.9990 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: 0.7980 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 overall best weight: 0.5696 ------------------------------------------------------------------------------- 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 = 0.4005 r_free = 0.4005 target = 0.089039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.075508 restraints weight = 16647.412| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 4.66 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3185 Z= 0.137 Angle : 0.594 5.950 4645 Z= 0.342 Chirality : 0.043 0.248 577 Planarity : 0.004 0.038 328 Dihedral : 24.770 165.951 1330 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 1.88 % Allowed : 23.12 % Favored : 75.00 % 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: -2.08 (0.67), residues: 174 helix: 0.87 (0.73), residues: 50 sheet: -2.06 (1.50), residues: 12 loop : -2.55 (0.64), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 121 TYR 0.005 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 0.00241 / 0.14 ( 3184) covalent geometry : angle 0.59405 / 0.34 ( 4645) hydrogen bonds : bond 0.08455 / 8.47 ( 80) hydrogen bonds : angle 4.66385 / 5.94 ( 187) Misc. bond : bond 0.00530 / 0.26 ( 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 : 0.047 Fit side-chains revert: symmetry clash REVERT: B 124 SER cc_start: 0.9321 (p) cc_final: 0.8951 (t) REVERT: B 208 ILE cc_start: 0.5289 (OUTLIER) cc_final: 0.4620 (pt) REVERT: B 215 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.7925 (tppp) REVERT: B 253 GLN cc_start: 0.8956 (tm-30) cc_final: 0.8457 (tm-30) REVERT: B 254 LEU cc_start: 0.9484 (mt) cc_final: 0.8920 (mt) outliers start: 3 outliers final: 1 residues processed: 31 average time/residue: 0.0448 time to fit residues: 1.7017 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 : 0.044 ------------------------------------------------------------------------------- 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: 10.0000 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 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 = 0.3944 r_free = 0.3944 target = 0.085095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.071550 restraints weight = 16847.386| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 4.50 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3185 Z= 0.174 Angle : 0.579 6.084 4645 Z= 0.327 Chirality : 0.040 0.223 577 Planarity : 0.006 0.054 328 Dihedral : 24.764 166.398 1330 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 3.75 % Allowed : 24.38 % 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: -1.84 (0.68), residues: 174 helix: 1.45 (0.77), residues: 50 sheet: -1.93 (1.46), residues: 12 loop : -2.61 (0.62), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 213 TYR 0.012 0.002 TYR B 123 PHE 0.020 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 0.00339 / 0.17 ( 3184) covalent geometry : angle 0.57948 / 0.33 ( 4645) hydrogen bonds : bond 0.07098 / 7.40 ( 80) hydrogen bonds : angle 4.66256 / 5.91 ( 187) Misc. bond : bond 0.00235 / 0.12 ( 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 32 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.079 Fit side-chains revert: symmetry clash REVERT: B 115 LEU cc_start: 0.9171 (tt) cc_final: 0.8948 (tt) REVERT: B 124 SER cc_start: 0.9403 (p) cc_final: 0.9081 (t) REVERT: B 215 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.7898 (tppp) REVERT: B 253 GLN cc_start: 0.8974 (tm-30) cc_final: 0.8457 (tm-30) REVERT: B 254 LEU cc_start: 0.9520 (mt) cc_final: 0.8968 (mt) outliers start: 6 outliers final: 2 residues processed: 31 average time/residue: 0.0546 time to fit residues: 2.1055 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 : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 245 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: 3.9990 chunk 0 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 0.0770 chunk 12 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.085902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.072437 restraints weight = 16929.297| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 4.67 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 3185 Z= 0.117 Angle : 0.569 8.659 4645 Z= 0.313 Chirality : 0.038 0.240 577 Planarity : 0.004 0.039 328 Dihedral : 24.613 168.547 1328 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 2.50 % Allowed : 25.00 % Favored : 72.50 % 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: -1.69 (0.68), residues: 174 helix: 1.60 (0.77), residues: 50 sheet: -1.80 (1.56), residues: 12 loop : -2.53 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 121 TYR 0.004 0.001 TYR B 123 PHE 0.007 0.001 PHE B 259 TRP 0.002 0.000 TRP B 160 HIS 0.002 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.12 ( 3184) covalent geometry : angle 0.56886 / 0.31 ( 4645) hydrogen bonds : bond 0.06710 / 6.77 ( 80) hydrogen bonds : angle 4.29262 / 5.35 ( 187) Misc. bond : bond 0.00017 / 0.01 ( 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 28 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.043 Fit side-chains REVERT: B 124 SER cc_start: 0.9369 (p) cc_final: 0.9028 (t) REVERT: B 215 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.7972 (tppp) REVERT: B 253 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8482 (tm-30) REVERT: B 254 LEU cc_start: 0.9510 (mt) cc_final: 0.8929 (mt) outliers start: 4 outliers final: 2 residues processed: 27 average time/residue: 0.0367 time to fit residues: 1.2585 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 : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 245 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.082512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.068534 restraints weight = 16687.166| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 4.51 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3185 Z= 0.177 Angle : 0.619 9.392 4645 Z= 0.340 Chirality : 0.040 0.223 577 Planarity : 0.006 0.058 328 Dihedral : 24.526 176.419 1328 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.07 % Favored : 87.93 % Rotamer: Outliers : 4.38 % Allowed : 25.62 % 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: -1.88 (0.66), residues: 174 helix: 1.30 (0.74), residues: 50 sheet: -1.84 (1.53), residues: 12 loop : -2.59 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 243 TYR 0.014 0.002 TYR B 123 PHE 0.010 0.002 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 0.00334 / 0.18 ( 3184) covalent geometry : angle 0.61928 / 0.34 ( 4645) hydrogen bonds : bond 0.06847 / 7.21 ( 80) hydrogen bonds : angle 4.44377 / 5.68 ( 187) Misc. bond : bond 0.00086 / 0.04 ( 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 30 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.044 Fit side-chains revert: symmetry clash REVERT: B 121 ARG cc_start: 0.9354 (OUTLIER) cc_final: 0.8991 (mtm-85) REVERT: B 124 SER cc_start: 0.9411 (p) cc_final: 0.9133 (t) REVERT: B 215 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8010 (tppp) REVERT: B 253 GLN cc_start: 0.8972 (tm-30) cc_final: 0.8453 (tm-30) REVERT: B 254 LEU cc_start: 0.9519 (mt) cc_final: 0.8953 (mt) outliers start: 7 outliers final: 3 residues processed: 27 average time/residue: 0.0637 time to fit residues: 2.0470 Evaluate side-chains 27 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.070 ------------------------------------------------------------------------------- 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 215 LYS Chi-restraints excluded: chain B residue 243 ARG 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: 0.7980 chunk 21 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 6 optimal weight: 20.0000 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3942 r_free = 0.3942 target = 0.084034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.069539 restraints weight = 16647.563| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 4.74 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 3185 Z= 0.127 Angle : 0.572 7.382 4645 Z= 0.317 Chirality : 0.039 0.264 577 Planarity : 0.004 0.038 328 Dihedral : 24.490 174.996 1328 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 5.00 % Allowed : 27.50 % Favored : 67.50 % 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: -1.80 (0.67), residues: 174 helix: 1.45 (0.78), residues: 50 sheet: -1.66 (1.63), residues: 12 loop : -2.60 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 243 TYR 0.004 0.001 TYR B 203 PHE 0.010 0.001 PHE B 259 TRP 0.001 0.000 TRP B 160 HIS 0.002 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 3184) covalent geometry : angle 0.57174 / 0.32 ( 4645) hydrogen bonds : bond 0.06192 / 6.10 ( 80) hydrogen bonds : angle 4.30174 / 5.43 ( 187) Misc. bond : bond 0.00030 / 0.02 ( 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: 8 poor density : 25 time to evaluate : 0.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 124 SER cc_start: 0.9379 (p) cc_final: 0.9047 (t) REVERT: B 215 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8047 (tppp) REVERT: B 253 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8485 (tm-30) REVERT: B 254 LEU cc_start: 0.9530 (mt) cc_final: 0.8953 (mt) outliers start: 8 outliers final: 4 residues processed: 29 average time/residue: 0.0550 time to fit residues: 1.9188 Evaluate side-chains 28 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 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 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: 6.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 chunk 7 optimal weight: 4.9990 chunk 18 optimal weight: 0.0970 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.081759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.067834 restraints weight = 17182.440| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 4.56 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3341 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= 0.159 Angle : 0.583 5.940 4645 Z= 0.324 Chirality : 0.039 0.229 577 Planarity : 0.004 0.035 328 Dihedral : 24.492 179.384 1328 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.92 % Favored : 89.08 % Rotamer: Outliers : 5.62 % Allowed : 28.75 % 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: -2.06 (0.66), residues: 174 helix: 1.29 (0.76), residues: 50 sheet: -1.82 (1.66), residues: 12 loop : -2.80 (0.58), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 243 TYR 0.010 0.001 TYR B 123 PHE 0.012 0.002 PHE B 173 TRP 0.001 0.000 TRP B 160 HIS 0.007 0.002 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 ( 3184) covalent geometry : angle 0.58314 / 0.32 ( 4645) hydrogen bonds : bond 0.06122 / 6.25 ( 80) hydrogen bonds : angle 4.38198 / 5.54 ( 187) Misc. bond : bond 0.00067 / 0.03 ( 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 34 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.078 Fit side-chains revert: symmetry clash REVERT: B 121 ARG cc_start: 0.9349 (OUTLIER) cc_final: 0.8974 (mtm-85) REVERT: B 124 SER cc_start: 0.9433 (p) cc_final: 0.9156 (t) REVERT: B 215 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.7998 (tptm) REVERT: B 253 GLN cc_start: 0.8992 (tm-30) cc_final: 0.8470 (tm-30) REVERT: B 254 LEU cc_start: 0.9523 (mt) cc_final: 0.8952 (mt) outliers start: 9 outliers final: 6 residues processed: 31 average time/residue: 0.0578 time to fit residues: 2.1713 Evaluate side-chains 31 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.045 ------------------------------------------------------------------------------- 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 118 GLN Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 245 VAL 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: 0.6980 chunk 3 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.082067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.067304 restraints weight = 17048.492| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 4.78 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3185 Z= 0.136 Angle : 0.570 6.953 4645 Z= 0.317 Chirality : 0.039 0.229 577 Planarity : 0.004 0.035 328 Dihedral : 24.551 177.917 1328 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.92 % Favored : 89.08 % Rotamer: Outliers : 6.25 % Allowed : 29.38 % 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: -2.02 (0.65), residues: 174 helix: 1.25 (0.76), residues: 50 sheet: -1.77 (1.66), residues: 12 loop : -2.73 (0.58), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 230 TYR 0.007 0.001 TYR B 123 PHE 0.015 0.003 PHE B 140 TRP 0.001 0.001 TRP B 160 HIS 0.003 0.001 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 ( 3184) covalent geometry : angle 0.56996 / 0.32 ( 4645) hydrogen bonds : bond 0.05744 / 5.63 ( 80) hydrogen bonds : angle 4.28806 / 5.41 ( 187) Misc. bond : bond 0.00024 / 0.01 ( 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 33 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 23 time to evaluate : 0.046 Fit side-chains revert: symmetry clash REVERT: B 121 ARG cc_start: 0.9350 (OUTLIER) cc_final: 0.8889 (mtt90) REVERT: B 124 SER cc_start: 0.9394 (p) cc_final: 0.9068 (t) REVERT: B 162 HIS cc_start: 0.8246 (OUTLIER) cc_final: 0.8040 (m90) REVERT: B 215 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.7980 (tptm) REVERT: B 253 GLN cc_start: 0.9039 (tm-30) cc_final: 0.8513 (tm-30) REVERT: B 254 LEU cc_start: 0.9536 (mt) cc_final: 0.8972 (mt) outliers start: 10 outliers final: 6 residues processed: 30 average time/residue: 0.0524 time to fit residues: 1.8890 Evaluate side-chains 32 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 23 time to evaluate : 0.054 ------------------------------------------------------------------------------- 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 118 GLN Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 18 optimal weight: 0.0670 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 3 optimal weight: 20.0000 chunk 14 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 GLN ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.083654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.068982 restraints weight = 16944.544| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 4.89 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3185 Z= 0.107 Angle : 0.552 7.769 4645 Z= 0.303 Chirality : 0.038 0.228 577 Planarity : 0.004 0.035 328 Dihedral : 24.455 176.378 1328 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 5.00 % Allowed : 29.38 % 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: -1.86 (0.66), residues: 174 helix: 1.26 (0.78), residues: 50 sheet: -1.28 (1.78), residues: 12 loop : -2.61 (0.58), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 127 TYR 0.004 0.001 TYR B 203 PHE 0.012 0.002 PHE B 259 TRP 0.002 0.001 TRP B 160 HIS 0.001 0.000 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.11 ( 3184) covalent geometry : angle 0.55175 / 0.30 ( 4645) hydrogen bonds : bond 0.05250 / 4.82 ( 80) hydrogen bonds : angle 4.19486 / 5.15 ( 187) Misc. bond : bond 0.00006 / 0.00 ( 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: 8 poor density : 26 time to evaluate : 0.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 121 ARG cc_start: 0.9329 (OUTLIER) cc_final: 0.9009 (mtt90) REVERT: B 124 SER cc_start: 0.9358 (p) cc_final: 0.9036 (t) REVERT: B 253 GLN cc_start: 0.9034 (tm-30) cc_final: 0.8530 (tm-30) REVERT: B 254 LEU cc_start: 0.9529 (mt) cc_final: 0.8958 (mt) outliers start: 8 outliers final: 6 residues processed: 31 average time/residue: 0.0762 time to fit residues: 2.8098 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 : 0.043 ------------------------------------------------------------------------------- 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 171 ILE Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 HIS 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: 5.9990 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 0.0970 chunk 6 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.082254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.067468 restraints weight = 16788.741| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 4.80 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3185 Z= 0.135 Angle : 0.556 6.894 4645 Z= 0.311 Chirality : 0.038 0.227 577 Planarity : 0.004 0.034 328 Dihedral : 24.467 177.655 1328 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.07 % Favored : 87.93 % 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: -2.10 (0.66), residues: 174 helix: 1.08 (0.75), residues: 50 sheet: -1.99 (1.23), residues: 22 loop : -2.71 (0.61), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 230 TYR 0.007 0.001 TYR B 123 PHE 0.009 0.002 PHE B 165 TRP 0.003 0.001 TRP B 160 HIS 0.002 0.001 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 ( 3184) covalent geometry : angle 0.55591 / 0.31 ( 4645) hydrogen bonds : bond 0.05312 / 5.18 ( 80) hydrogen bonds : angle 4.26085 / 5.26 ( 187) Misc. bond : bond 0.00033 / 0.02 ( 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: 8 poor density : 23 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: B 124 SER cc_start: 0.9399 (p) cc_final: 0.9090 (t) REVERT: B 215 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.7995 (tptm) REVERT: B 253 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8544 (tm-30) REVERT: B 254 LEU cc_start: 0.9538 (mt) cc_final: 0.8976 (mt) outliers start: 8 outliers final: 7 residues processed: 28 average time/residue: 0.0670 time to fit residues: 2.2589 Evaluate side-chains 30 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.074 ------------------------------------------------------------------------------- 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 171 ILE Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 16 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 9 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.081634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.066820 restraints weight = 17030.436| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 4.81 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3185 Z= 0.141 Angle : 0.597 8.163 4645 Z= 0.327 Chirality : 0.039 0.230 577 Planarity : 0.005 0.037 328 Dihedral : 24.531 177.114 1328 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 5.00 % Allowed : 31.25 % Favored : 63.75 % 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: -2.07 (0.66), residues: 174 helix: 1.20 (0.76), residues: 50 sheet: -2.10 (1.20), residues: 22 loop : -2.71 (0.61), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 244 TYR 0.007 0.001 TYR B 123 PHE 0.009 0.002 PHE B 165 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 0.00284 / 0.14 ( 3184) covalent geometry : angle 0.59693 / 0.33 ( 4645) hydrogen bonds : bond 0.05355 / 5.23 ( 80) hydrogen bonds : angle 4.29642 / 5.40 ( 187) Misc. bond : bond 0.00042 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 619.89 seconds wall clock time: 11 minutes 14.65 seconds (674.65 seconds total)