Starting phenix.real_space_refine on Sat Apr 4 22:20:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u5q_63879/04_2026/9u5q_63879.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u5q_63879/04_2026/9u5q_63879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u5q_63879/04_2026/9u5q_63879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u5q_63879/04_2026/9u5q_63879.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u5q_63879/04_2026/9u5q_63879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u5q_63879/04_2026/9u5q_63879.map" } resolution = 3.35 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= 0.008 sd= 1.147 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 75 5.49 5 S 15 5.16 5 C 2678 2.51 5 N 812 2.21 5 O 1142 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-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4722 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1382 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain: "B" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 973 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 2, 'TRANS': 124} Chain: "C" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 780 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "R" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1587 Classifications: {'RNA': 75} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 30, 'rna3p_pyr': 36} Link IDs: {'rna2p': 8, 'rna3p': 66} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.30, per 1000 atoms: 0.28 Number of scatterers: 4722 At special positions: 0 Unit cell: (88.32, 73.92, 132.48, 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 15 16.00 P 75 15.00 O 1142 8.00 N 812 7.00 C 2678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 403.0 milliseconds 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 730 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 11.4% alpha, 47.7% beta 25 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 3 through 14 Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.685A pdb=" N ILE A 90 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.775A pdb=" N GLN A 145 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS A 146 " --> pdb=" O THR A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.558A pdb=" N TYR A 177 " --> pdb=" O LYS A 174 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE A 178 " --> pdb=" O LYS A 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 178' Processing helix chain 'B' and resid 30 through 34 removed outlier: 3.622A pdb=" N SER B 33 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR B 34 " --> pdb=" O PHE B 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 34' Processing helix chain 'C' and resid 26 through 30 removed outlier: 3.643A pdb=" N ASP C 29 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.798A pdb=" N ASP C 81 " --> pdb=" O GLN C 78 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU C 82 " --> pdb=" O ALA C 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 78 through 82' Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 20 removed outlier: 3.519A pdb=" N LEU A 28 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A 34 " --> pdb=" O ILE A 30 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU A 72 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP A 58 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP A 78 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 56 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 126 removed outlier: 6.980A pdb=" N MET A 120 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE A 135 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY A 122 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 133 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ARG A 133 " --> pdb=" O GLN A 172 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ALA A 171 " --> pdb=" O HIS A 160 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N HIS A 160 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU A 150 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA A 99 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 115 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER A 105 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 10 Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 14 removed outlier: 6.098A pdb=" N ARG B 40 " --> pdb=" O TRP B 49 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N TRP B 49 " --> pdb=" O ARG B 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 13 through 14 removed outlier: 4.339A pdb=" N VAL B 117 " --> pdb=" O ARG B 100 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 9 through 11 removed outlier: 3.596A pdb=" N THR C 104 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 17 through 23 Processing sheet with id=AA8, first strand: chain 'C' and resid 44 through 47 removed outlier: 6.848A pdb=" N TRP C 34 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR C 94 " --> pdb=" O ASP C 91 " (cutoff:3.500A) 126 hydrogen bonds defined for protein. 315 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 0.57 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1206 1.33 - 1.45: 1328 1.45 - 1.57: 2262 1.57 - 1.69: 148 1.69 - 1.81: 22 Bond restraints: 4966 Sorted by residual: bond pdb=" CA ARG A 84 " pdb=" C ARG A 84 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.24e-02 6.50e+03 1.17e+01 bond pdb=" P A R 13 " pdb=" OP2 A R 13 " ideal model delta sigma weight residual 1.485 1.527 -0.042 2.00e-02 2.50e+03 4.45e+00 bond pdb=" P G R 12 " pdb=" OP2 G R 12 " ideal model delta sigma weight residual 1.485 1.526 -0.041 2.00e-02 2.50e+03 4.28e+00 bond pdb=" C ARG A 84 " pdb=" N ASP A 85 " ideal model delta sigma weight residual 1.331 1.302 0.029 1.44e-02 4.82e+03 4.08e+00 bond pdb=" N VAL C 105 " pdb=" CA VAL C 105 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.90e-02 2.77e+03 4.04e+00 ... (remaining 4961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 6706 1.71 - 3.41: 321 3.41 - 5.12: 36 5.12 - 6.83: 14 6.83 - 8.54: 2 Bond angle restraints: 7079 Sorted by residual: angle pdb=" CA THR C 104 " pdb=" C THR C 104 " pdb=" O THR C 104 " ideal model delta sigma weight residual 120.36 124.63 -4.27 1.08e+00 8.57e-01 1.56e+01 angle pdb=" O3' A R 4 " pdb=" P A R 5 " pdb=" O5' A R 5 " ideal model delta sigma weight residual 104.00 98.81 5.19 1.50e+00 4.44e-01 1.20e+01 angle pdb=" O3' U R 14 " pdb=" C3' U R 14 " pdb=" C2' U R 14 " ideal model delta sigma weight residual 113.70 118.12 -4.42 1.50e+00 4.44e-01 8.69e+00 angle pdb=" C3' U R 14 " pdb=" O3' U R 14 " pdb=" P G R 15 " ideal model delta sigma weight residual 120.20 124.29 -4.09 1.50e+00 4.44e-01 7.43e+00 angle pdb=" O THR C 104 " pdb=" C THR C 104 " pdb=" N VAL C 105 " ideal model delta sigma weight residual 123.30 120.08 3.22 1.19e+00 7.06e-01 7.31e+00 ... (remaining 7074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.95: 2660 22.95 - 45.90: 236 45.90 - 68.84: 139 68.84 - 91.79: 22 91.79 - 114.74: 1 Dihedral angle restraints: 3058 sinusoidal: 1901 harmonic: 1157 Sorted by residual: dihedral pdb=" O4' A R 59 " pdb=" C1' A R 59 " pdb=" N9 A R 59 " pdb=" C4 A R 59 " ideal model delta sinusoidal sigma weight residual 254.00 178.29 75.71 1 1.70e+01 3.46e-03 2.50e+01 dihedral pdb=" O4' U R 60 " pdb=" C1' U R 60 " pdb=" N1 U R 60 " pdb=" C2 U R 60 " ideal model delta sinusoidal sigma weight residual 232.00 178.74 53.26 1 1.70e+01 3.46e-03 1.33e+01 dihedral pdb=" O4' A R 4 " pdb=" C1' A R 4 " pdb=" N9 A R 4 " pdb=" C4 A R 4 " ideal model delta sinusoidal sigma weight residual -106.00 -154.62 48.62 1 1.70e+01 3.46e-03 1.13e+01 ... (remaining 3055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 688 0.101 - 0.203: 158 0.203 - 0.304: 2 0.304 - 0.406: 4 0.406 - 0.507: 5 Chirality restraints: 857 Sorted by residual: chirality pdb=" P C R 82 " pdb=" OP1 C R 82 " pdb=" OP2 C R 82 " pdb=" O5' C R 82 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.43e+00 chirality pdb=" P A R 4 " pdb=" OP1 A R 4 " pdb=" OP2 A R 4 " pdb=" O5' A R 4 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 6.03e+00 chirality pdb=" P C R 25 " pdb=" OP1 C R 25 " pdb=" OP2 C R 25 " pdb=" O5' C R 25 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.79e+00 ... (remaining 854 not shown) Planarity restraints: 632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 83 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C PHE A 83 " -0.066 2.00e-02 2.50e+03 pdb=" O PHE A 83 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG A 84 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 7 " -0.042 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO C 8 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 8 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 8 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 71 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.03e+00 pdb=" C GLU A 71 " -0.030 2.00e-02 2.50e+03 pdb=" O GLU A 71 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU A 72 " 0.010 2.00e-02 2.50e+03 ... (remaining 629 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 740 2.76 - 3.30: 3870 3.30 - 3.83: 7900 3.83 - 4.37: 9545 4.37 - 4.90: 15180 Nonbonded interactions: 37235 Sorted by model distance: nonbonded pdb=" O2' U R 14 " pdb=" OP1 G R 15 " model vdw 2.227 3.040 nonbonded pdb=" OP2 C R 10 " pdb=" O2' U R 42 " model vdw 2.342 3.040 nonbonded pdb=" OH TYR C 2 " pdb=" O ASP C 25 " model vdw 2.344 3.040 nonbonded pdb=" N6 A R 36 " pdb=" O2 C R 51 " model vdw 2.366 3.120 nonbonded pdb=" NH1 ARG B 69 " pdb=" O SER B 87 " model vdw 2.371 3.120 ... (remaining 37230 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 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: 0.020 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.230 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5181 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 : 0.005 0.042 4966 Z= 0.318 Angle : 0.817 8.537 7079 Z= 0.430 Chirality : 0.082 0.507 857 Planarity : 0.005 0.064 632 Dihedral : 20.317 114.738 2328 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 14.87 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.43), residues: 405 helix: 1.97 (1.78), residues: 11 sheet: 1.08 (0.40), residues: 182 loop : -0.90 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 84 TYR 0.011 0.001 TYR B 97 PHE 0.011 0.001 PHE B 70 TRP 0.012 0.001 TRP C 90 HIS 0.002 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 4966) covalent geometry : angle 0.81705 ( 7079) hydrogen bonds : bond 0.14654 ( 185) hydrogen bonds : angle 5.01367 ( 435) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.140 Fit side-chains REVERT: B 103 LYS cc_start: 0.8231 (mmpt) cc_final: 0.7925 (mmtt) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0674 time to fit residues: 4.6666 Evaluate side-chains 44 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 31 HIS B 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.208624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.186545 restraints weight = 7993.165| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 2.24 r_work: 0.4235 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6155 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4966 Z= 0.195 Angle : 0.677 7.049 7079 Z= 0.346 Chirality : 0.041 0.222 857 Planarity : 0.005 0.046 632 Dihedral : 20.533 126.449 1622 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.04 % Allowed : 17.49 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.41), residues: 405 helix: 2.28 (1.44), residues: 11 sheet: 1.23 (0.41), residues: 153 loop : -1.18 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 74 TYR 0.013 0.002 TYR A 139 PHE 0.009 0.002 PHE A 178 TRP 0.022 0.003 TRP B 38 HIS 0.006 0.002 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 4966) covalent geometry : angle 0.67695 ( 7079) hydrogen bonds : bond 0.05356 ( 185) hydrogen bonds : angle 4.68590 ( 435) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 35 CYS cc_start: 0.7106 (p) cc_final: 0.6902 (p) REVERT: A 115 VAL cc_start: 0.7595 (m) cc_final: 0.7356 (m) REVERT: C 9 SER cc_start: 0.7474 (p) cc_final: 0.7012 (m) REVERT: C 44 VAL cc_start: 0.8477 (t) cc_final: 0.8105 (m) outliers start: 7 outliers final: 5 residues processed: 54 average time/residue: 0.0523 time to fit residues: 3.8906 Evaluate side-chains 52 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 47 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS A 106 ASN A 160 HIS B 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.187844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.168026 restraints weight = 7467.888| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 2.17 r_work: 0.4028 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.7509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 4966 Z= 0.296 Angle : 0.846 7.521 7079 Z= 0.426 Chirality : 0.047 0.241 857 Planarity : 0.006 0.044 632 Dihedral : 20.856 137.200 1622 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.37 % Allowed : 16.33 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.41), residues: 405 helix: 2.32 (1.58), residues: 11 sheet: 0.87 (0.41), residues: 155 loop : -1.28 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 69 TYR 0.025 0.003 TYR A 60 PHE 0.027 0.004 PHE A 25 TRP 0.016 0.003 TRP B 38 HIS 0.010 0.003 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00631 ( 4966) covalent geometry : angle 0.84571 ( 7079) hydrogen bonds : bond 0.07868 ( 185) hydrogen bonds : angle 4.76306 ( 435) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.132 Fit side-chains REVERT: A 22 LYS cc_start: 0.8069 (mmmt) cc_final: 0.7844 (mmtm) REVERT: A 35 CYS cc_start: 0.7434 (p) cc_final: 0.7220 (p) REVERT: B 65 SER cc_start: 0.7181 (OUTLIER) cc_final: 0.6881 (t) REVERT: B 115 MET cc_start: 0.6086 (mpp) cc_final: 0.5744 (mtt) REVERT: C 9 SER cc_start: 0.7228 (p) cc_final: 0.6949 (m) outliers start: 15 outliers final: 9 residues processed: 53 average time/residue: 0.0419 time to fit residues: 3.2892 Evaluate side-chains 49 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 92 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 28 optimal weight: 0.5980 chunk 12 optimal weight: 30.0000 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 33 optimal weight: 0.0030 chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN B 8 GLN C 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.189427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.169994 restraints weight = 7516.102| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 2.07 r_work: 0.4058 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 0.7810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4966 Z= 0.159 Angle : 0.635 6.456 7079 Z= 0.323 Chirality : 0.040 0.242 857 Planarity : 0.005 0.038 632 Dihedral : 20.474 136.810 1622 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.92 % Allowed : 21.28 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.42), residues: 405 helix: 3.18 (1.60), residues: 11 sheet: 0.85 (0.40), residues: 169 loop : -1.04 (0.40), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 40 TYR 0.014 0.002 TYR A 139 PHE 0.016 0.002 PHE A 25 TRP 0.010 0.002 TRP C 90 HIS 0.005 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 4966) covalent geometry : angle 0.63453 ( 7079) hydrogen bonds : bond 0.04959 ( 185) hydrogen bonds : angle 4.33339 ( 435) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.168 Fit side-chains REVERT: A 15 ILE cc_start: 0.8217 (mt) cc_final: 0.7955 (mt) REVERT: B 65 SER cc_start: 0.6900 (OUTLIER) cc_final: 0.6617 (t) REVERT: C 9 SER cc_start: 0.7121 (p) cc_final: 0.6824 (m) outliers start: 10 outliers final: 6 residues processed: 54 average time/residue: 0.0496 time to fit residues: 3.7233 Evaluate side-chains 50 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 62 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN B 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.185328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.166433 restraints weight = 7580.465| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.10 r_work: 0.4012 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.8515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4966 Z= 0.198 Angle : 0.710 7.193 7079 Z= 0.358 Chirality : 0.042 0.247 857 Planarity : 0.005 0.064 632 Dihedral : 20.524 138.435 1622 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.08 % Allowed : 23.03 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.41), residues: 405 helix: 3.02 (1.66), residues: 11 sheet: 0.88 (0.41), residues: 160 loop : -1.06 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 69 TYR 0.015 0.002 TYR A 60 PHE 0.021 0.002 PHE A 25 TRP 0.012 0.002 TRP C 90 HIS 0.008 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 4966) covalent geometry : angle 0.70961 ( 7079) hydrogen bonds : bond 0.05825 ( 185) hydrogen bonds : angle 4.40652 ( 435) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.105 Fit side-chains REVERT: A 15 ILE cc_start: 0.8203 (mt) cc_final: 0.7976 (mt) REVERT: B 65 SER cc_start: 0.6966 (OUTLIER) cc_final: 0.6726 (t) REVERT: C 9 SER cc_start: 0.7223 (p) cc_final: 0.6989 (m) outliers start: 14 outliers final: 8 residues processed: 54 average time/residue: 0.0576 time to fit residues: 4.2575 Evaluate side-chains 50 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 21 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 0.0870 chunk 31 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN B 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.186371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.167540 restraints weight = 7619.534| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 2.14 r_work: 0.4030 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.8689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4966 Z= 0.150 Angle : 0.631 7.116 7079 Z= 0.319 Chirality : 0.040 0.229 857 Planarity : 0.005 0.034 632 Dihedral : 20.428 138.822 1622 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.08 % Allowed : 23.62 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.42), residues: 405 helix: 3.41 (1.63), residues: 11 sheet: 0.70 (0.40), residues: 173 loop : -0.77 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 69 TYR 0.010 0.001 TYR A 139 PHE 0.014 0.002 PHE A 25 TRP 0.010 0.001 TRP C 90 HIS 0.007 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 4966) covalent geometry : angle 0.63120 ( 7079) hydrogen bonds : bond 0.04766 ( 185) hydrogen bonds : angle 4.19857 ( 435) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.136 Fit side-chains REVERT: A 15 ILE cc_start: 0.8223 (mt) cc_final: 0.8018 (mt) REVERT: B 8 GLN cc_start: 0.6373 (OUTLIER) cc_final: 0.5998 (mp10) REVERT: B 93 THR cc_start: 0.7282 (m) cc_final: 0.7041 (p) REVERT: C 9 SER cc_start: 0.7257 (p) cc_final: 0.7012 (m) outliers start: 14 outliers final: 11 residues processed: 52 average time/residue: 0.0671 time to fit residues: 4.5337 Evaluate side-chains 54 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 64 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.180375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.163101 restraints weight = 7571.630| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 1.97 r_work: 0.3987 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3845 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.9270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 4966 Z= 0.253 Angle : 0.810 7.629 7079 Z= 0.405 Chirality : 0.045 0.253 857 Planarity : 0.006 0.076 632 Dihedral : 20.845 133.796 1622 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 5.54 % Allowed : 21.57 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.41), residues: 405 helix: 2.92 (1.72), residues: 11 sheet: 0.54 (0.41), residues: 160 loop : -1.12 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 69 TYR 0.016 0.002 TYR A 139 PHE 0.025 0.003 PHE A 25 TRP 0.014 0.002 TRP C 90 HIS 0.010 0.002 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 4966) covalent geometry : angle 0.80994 ( 7079) hydrogen bonds : bond 0.06825 ( 185) hydrogen bonds : angle 4.65786 ( 435) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 51 time to evaluate : 0.134 Fit side-chains REVERT: A 159 ILE cc_start: 0.5677 (OUTLIER) cc_final: 0.5088 (mm) REVERT: A 172 GLN cc_start: 0.6711 (OUTLIER) cc_final: 0.5973 (tp40) REVERT: B 65 SER cc_start: 0.7130 (OUTLIER) cc_final: 0.6924 (t) outliers start: 19 outliers final: 13 residues processed: 60 average time/residue: 0.0607 time to fit residues: 4.9671 Evaluate side-chains 60 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 105 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 3 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 34 optimal weight: 0.0060 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN B 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.184225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.165910 restraints weight = 7594.774| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 2.12 r_work: 0.4012 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.9276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4966 Z= 0.144 Angle : 0.617 6.143 7079 Z= 0.314 Chirality : 0.039 0.228 857 Planarity : 0.004 0.035 632 Dihedral : 20.439 136.613 1622 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.08 % Allowed : 24.20 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.42), residues: 405 helix: 3.50 (1.64), residues: 11 sheet: 0.50 (0.40), residues: 173 loop : -0.69 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.010 0.001 TYR A 139 PHE 0.013 0.002 PHE A 25 TRP 0.010 0.001 TRP C 90 HIS 0.006 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4966) covalent geometry : angle 0.61693 ( 7079) hydrogen bonds : bond 0.04651 ( 185) hydrogen bonds : angle 4.23613 ( 435) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.097 Fit side-chains REVERT: A 159 ILE cc_start: 0.5424 (OUTLIER) cc_final: 0.4896 (mm) REVERT: A 172 GLN cc_start: 0.6633 (OUTLIER) cc_final: 0.5866 (tp40) REVERT: B 8 GLN cc_start: 0.6348 (OUTLIER) cc_final: 0.5939 (mp10) REVERT: B 47 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7700 (mt) outliers start: 14 outliers final: 9 residues processed: 52 average time/residue: 0.0544 time to fit residues: 3.7714 Evaluate side-chains 56 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 64 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.181895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.164055 restraints weight = 7476.324| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 2.08 r_work: 0.3986 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.9472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4966 Z= 0.194 Angle : 0.700 6.627 7079 Z= 0.353 Chirality : 0.041 0.239 857 Planarity : 0.005 0.052 632 Dihedral : 20.631 134.554 1622 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.37 % Allowed : 24.20 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.42), residues: 405 helix: 3.15 (1.67), residues: 11 sheet: 0.58 (0.41), residues: 160 loop : -0.76 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 69 TYR 0.013 0.002 TYR A 139 PHE 0.018 0.002 PHE A 25 TRP 0.013 0.002 TRP C 90 HIS 0.008 0.002 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 4966) covalent geometry : angle 0.69958 ( 7079) hydrogen bonds : bond 0.05536 ( 185) hydrogen bonds : angle 4.39199 ( 435) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.123 Fit side-chains REVERT: A 159 ILE cc_start: 0.5464 (OUTLIER) cc_final: 0.4897 (mm) REVERT: A 172 GLN cc_start: 0.6641 (OUTLIER) cc_final: 0.5887 (tp40) outliers start: 15 outliers final: 12 residues processed: 51 average time/residue: 0.0681 time to fit residues: 4.5793 Evaluate side-chains 56 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 64 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 34 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 0.0040 chunk 7 optimal weight: 0.7980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN B 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.183905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.165952 restraints weight = 7500.786| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 2.06 r_work: 0.4016 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.9555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4966 Z= 0.144 Angle : 0.612 6.217 7079 Z= 0.312 Chirality : 0.039 0.228 857 Planarity : 0.004 0.036 632 Dihedral : 20.456 135.946 1622 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.08 % Allowed : 24.20 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.43), residues: 405 helix: 3.61 (1.65), residues: 11 sheet: 0.54 (0.41), residues: 173 loop : -0.44 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 53 TYR 0.009 0.001 TYR A 60 PHE 0.014 0.002 PHE A 25 TRP 0.011 0.001 TRP C 90 HIS 0.006 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 4966) covalent geometry : angle 0.61204 ( 7079) hydrogen bonds : bond 0.04508 ( 185) hydrogen bonds : angle 4.19634 ( 435) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.132 Fit side-chains REVERT: A 159 ILE cc_start: 0.5340 (OUTLIER) cc_final: 0.4787 (mm) REVERT: A 172 GLN cc_start: 0.6627 (OUTLIER) cc_final: 0.5848 (tp40) REVERT: B 47 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7758 (mt) outliers start: 14 outliers final: 11 residues processed: 50 average time/residue: 0.0546 time to fit residues: 3.7541 Evaluate side-chains 57 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 64 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.0040 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN B 8 GLN B 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.183792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.165978 restraints weight = 7512.128| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.04 r_work: 0.4016 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.9557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.126 4966 Z= 0.240 Angle : 1.141 59.115 7079 Z= 0.670 Chirality : 0.041 0.342 857 Planarity : 0.005 0.036 632 Dihedral : 20.459 135.957 1622 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.66 % Allowed : 25.36 % Favored : 69.97 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.43), residues: 405 helix: 3.60 (1.65), residues: 11 sheet: 0.54 (0.41), residues: 173 loop : -0.43 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.009 0.001 TYR A 60 PHE 0.015 0.002 PHE A 25 TRP 0.011 0.001 TRP C 90 HIS 0.006 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 4966) covalent geometry : angle 1.14079 ( 7079) hydrogen bonds : bond 0.04543 ( 185) hydrogen bonds : angle 4.18941 ( 435) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1167.53 seconds wall clock time: 20 minutes 42.71 seconds (1242.71 seconds total)