Starting phenix.real_space_refine on Wed Aug 5 08:10:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zmj_60249/08_2026/8zmj_60249.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zmj_60249/08_2026/8zmj_60249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zmj_60249/08_2026/8zmj_60249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zmj_60249/08_2026/8zmj_60249.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zmj_60249/08_2026/8zmj_60249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zmj_60249/08_2026/8zmj_60249.map" } resolution = 3.73 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= 0.009 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 168 5.49 5 S 40 5.16 5 C 5166 2.51 5 N 1589 2.21 5 O 2221 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s 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: 9184 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2795 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 15, 'TRANS': 332} Chain: "B" Number of atoms: 2795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2795 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 15, 'TRANS': 332} Chain: "C" Number of atoms: 3594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 3594 Classifications: {'RNA': 169} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 8, 'rna3p_pur': 79, 'rna3p_pyr': 74} Link IDs: {'rna2p': 15, 'rna3p': 153} Time building chain proxies: 2.00, per 1000 atoms: 0.22 Number of scatterers: 9184 At special positions: 0 Unit cell: (90.2, 116.44, 136.94, 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 40 16.00 P 168 15.00 O 2221 8.00 N 1589 7.00 C 5166 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: 0.92 Conformation dependent library (CDL) restraints added in 227.1 milliseconds 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1316 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 4 sheets defined 64.1% alpha, 7.3% beta 52 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 31 through 39 removed outlier: 4.052A pdb=" N PHE A 35 " --> pdb=" O PRO A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 58 Processing helix chain 'A' and resid 74 through 91 removed outlier: 3.907A pdb=" N LYS A 81 " --> pdb=" O GLN A 77 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 108 Processing helix chain 'A' and resid 114 through 132 Processing helix chain 'A' and resid 145 through 152 Processing helix chain 'A' and resid 152 through 167 Proline residue: A 158 - end of helix Processing helix chain 'A' and resid 168 through 175 Processing helix chain 'A' and resid 188 through 205 Proline residue: A 195 - end of helix removed outlier: 3.534A pdb=" N ASP A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 202 " --> pdb=" O GLN A 198 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE A 203 " --> pdb=" O CYS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 230 Processing helix chain 'A' and resid 268 through 279 Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 336 through 362 Proline residue: A 342 - end of helix Proline residue: A 354 - end of helix Processing helix chain 'A' and resid 362 through 375 Processing helix chain 'B' and resid 32 through 42 removed outlier: 3.645A pdb=" N VAL B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY B 42 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 58 Processing helix chain 'B' and resid 74 through 92 removed outlier: 3.563A pdb=" N GLY B 78 " --> pdb=" O HIS B 74 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS B 81 " --> pdb=" O GLN B 77 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 109 through 112 Processing helix chain 'B' and resid 113 through 132 removed outlier: 3.545A pdb=" N GLY B 132 " --> pdb=" O TRP B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 145 through 150 Processing helix chain 'B' and resid 156 through 167 Processing helix chain 'B' and resid 168 through 175 Processing helix chain 'B' and resid 188 through 205 Proline residue: B 195 - end of helix removed outlier: 3.812A pdb=" N PHE B 203 " --> pdb=" O CYS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 216 through 230 Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.865A pdb=" N SER B 262 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 278 Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 311 through 315 removed outlier: 3.635A pdb=" N GLY B 315 " --> pdb=" O ALA B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 333 removed outlier: 3.634A pdb=" N LEU B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 362 Proline residue: B 342 - end of helix Proline residue: B 354 - end of helix Processing helix chain 'B' and resid 362 through 375 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 46 removed outlier: 3.974A pdb=" N ILE A 46 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ILE A 238 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N CYS A 210 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N HIS A 241 " --> pdb=" O CYS A 210 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A 212 " --> pdb=" O HIS A 241 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL A 62 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLN A 211 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N TYR A 64 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N GLY A 213 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N GLY A 66 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N CYS A 63 " --> pdb=" O LYS A 96 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TRP A 98 " --> pdb=" O CYS A 63 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ASP A 65 " --> pdb=" O TRP A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 306 through 308 Processing sheet with id=AA3, first strand: chain 'B' and resid 44 through 46 removed outlier: 3.632A pdb=" N GLU B 44 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B 240 " --> pdb=" O GLU B 44 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 46 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE B 238 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N CYS B 210 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N CYS B 63 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TRP B 98 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP B 65 " --> pdb=" O TRP B 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 306 through 308 285 hydrogen bonds defined for protein. 819 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 129 hydrogen bonds 238 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 86 stacking parallelities Total time for adding SS restraints: 1.33 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1403 1.33 - 1.45: 3291 1.45 - 1.57: 4628 1.57 - 1.69: 336 1.69 - 1.81: 60 Bond restraints: 9718 Sorted by residual: bond pdb=" P G C 2 " pdb=" O5' G C 2 " ideal model delta sigma weight residual 1.593 1.626 -0.033 1.00e-02 1.00e+04 1.07e+01 bond pdb=" N ARG B 72 " pdb=" CA ARG B 72 " ideal model delta sigma weight residual 1.454 1.490 -0.035 1.23e-02 6.61e+03 8.30e+00 bond pdb=" N GLU B 268 " pdb=" CA GLU B 268 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.22e-02 6.72e+03 8.26e+00 bond pdb=" N VAL B 372 " pdb=" CA VAL B 372 " ideal model delta sigma weight residual 1.461 1.494 -0.032 1.17e-02 7.31e+03 7.65e+00 bond pdb=" N VAL B 263 " pdb=" CA VAL B 263 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.26e-02 6.30e+03 7.12e+00 ... (remaining 9713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 13205 1.95 - 3.90: 670 3.90 - 5.84: 44 5.84 - 7.79: 6 7.79 - 9.74: 2 Bond angle restraints: 13927 Sorted by residual: angle pdb=" O2 C C 42 " pdb=" C2 C C 42 " pdb=" N3 C C 42 " ideal model delta sigma weight residual 121.90 118.27 3.63 7.00e-01 2.04e+00 2.69e+01 angle pdb=" N ILE B 75 " pdb=" CA ILE B 75 " pdb=" C ILE B 75 " ideal model delta sigma weight residual 112.50 105.30 7.20 1.39e+00 5.18e-01 2.68e+01 angle pdb=" C GLY B 112 " pdb=" N ASP B 113 " pdb=" CA ASP B 113 " ideal model delta sigma weight residual 121.50 115.11 6.39 1.43e+00 4.89e-01 1.99e+01 angle pdb=" N1 C C 42 " pdb=" C2 C C 42 " pdb=" O2 C C 42 " ideal model delta sigma weight residual 118.90 121.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" CB ARG A 360 " pdb=" CG ARG A 360 " pdb=" CD ARG A 360 " ideal model delta sigma weight residual 111.30 121.04 -9.74 2.30e+00 1.89e-01 1.79e+01 ... (remaining 13922 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.13: 5485 30.13 - 60.27: 484 60.27 - 90.40: 159 90.40 - 120.54: 7 120.54 - 150.67: 3 Dihedral angle restraints: 6138 sinusoidal: 4106 harmonic: 2032 Sorted by residual: dihedral pdb=" O4' U C 45 " pdb=" C1' U C 45 " pdb=" N1 U C 45 " pdb=" C2 U C 45 " ideal model delta sinusoidal sigma weight residual 200.00 49.33 150.67 1 1.50e+01 4.44e-03 7.99e+01 dihedral pdb=" O4' U C 67 " pdb=" C1' U C 67 " pdb=" N1 U C 67 " pdb=" C2 U C 67 " ideal model delta sinusoidal sigma weight residual 200.00 51.47 148.53 1 1.50e+01 4.44e-03 7.91e+01 dihedral pdb=" O4' C C 167 " pdb=" C1' C C 167 " pdb=" N1 C C 167 " pdb=" C2 C C 167 " ideal model delta sinusoidal sigma weight residual 200.00 57.79 142.21 1 1.50e+01 4.44e-03 7.64e+01 ... (remaining 6135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1338 0.062 - 0.125: 158 0.125 - 0.187: 158 0.187 - 0.250: 14 0.250 - 0.312: 4 Chirality restraints: 1672 Sorted by residual: chirality pdb=" P G C 2 " pdb=" OP1 G C 2 " pdb=" OP2 G C 2 " pdb=" O5' G C 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.72 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA ILE B 99 " pdb=" N ILE B 99 " pdb=" C ILE B 99 " pdb=" CB ILE B 99 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA ILE B 75 " pdb=" N ILE B 75 " pdb=" C ILE B 75 " pdb=" CB ILE B 75 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1669 not shown) Planarity restraints: 1153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 128 " -0.020 2.00e-02 2.50e+03 1.50e-02 5.62e+00 pdb=" CG TRP B 128 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP B 128 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 128 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 128 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 128 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 128 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 128 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 128 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 128 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 67 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C PHE B 67 " 0.030 2.00e-02 2.50e+03 pdb=" O PHE B 67 " -0.012 2.00e-02 2.50e+03 pdb=" N GLU B 68 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 68 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C GLU B 68 " -0.029 2.00e-02 2.50e+03 pdb=" O GLU B 68 " 0.010 2.00e-02 2.50e+03 pdb=" N PRO B 69 " 0.010 2.00e-02 2.50e+03 ... (remaining 1150 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1075 2.74 - 3.28: 9541 3.28 - 3.82: 17719 3.82 - 4.36: 20885 4.36 - 4.90: 30314 Nonbonded interactions: 79534 Sorted by model distance: nonbonded pdb=" O6 G C 46 " pdb=" N4 C C 65 " model vdw 2.205 3.120 nonbonded pdb=" O4 U C 52 " pdb=" N6 A C 162 " model vdw 2.208 3.120 nonbonded pdb=" O PRO B 282 " pdb=" OH TYR B 330 " model vdw 2.223 3.040 nonbonded pdb=" O2' G C 96 " pdb=" O4' G C 97 " model vdw 2.227 3.040 nonbonded pdb=" OG SER B 311 " pdb=" OD1 ASP B 313 " model vdw 2.241 3.040 ... (remaining 79529 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 3.140 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.220 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 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 : 0.004 0.052 9718 Z= 0.280 Angle : 0.782 9.739 13927 Z= 0.573 Chirality : 0.060 0.312 1672 Planarity : 0.004 0.039 1153 Dihedral : 21.614 150.671 4822 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.49 % Allowed : 0.65 % Favored : 98.86 % 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: 0.66 (0.34), residues: 692 helix: 0.84 (0.27), residues: 400 sheet: -1.69 (0.67), residues: 68 loop : 0.75 (0.46), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 360 TYR 0.017 0.002 TYR B 123 PHE 0.019 0.001 PHE A 359 TRP 0.040 0.002 TRP B 128 HIS 0.011 0.002 HIS B 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.28 ( 9718) covalent geometry : angle 0.78176 / 0.57 (13927) hydrogen bonds : bond 0.14274 / 8.95 ( 414) hydrogen bonds : angle 6.47670 / 4.69 ( 1057) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.7767 (mmm) cc_final: 0.6852 (mmm) outliers start: 3 outliers final: 0 residues processed: 121 average time/residue: 0.0823 time to fit residues: 14.0475 Evaluate side-chains 74 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.0270 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 HIS A 242 HIS A 358 HIS ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.059082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.042433 restraints weight = 68592.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.043569 restraints weight = 42753.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.044103 restraints weight = 31437.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.044745 restraints weight = 26390.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.045094 restraints weight = 22961.182| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9718 Z= 0.149 Angle : 0.595 8.370 13927 Z= 0.321 Chirality : 0.037 0.187 1672 Planarity : 0.005 0.033 1153 Dihedral : 22.889 162.746 3356 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.97 % Allowed : 11.04 % Favored : 87.99 % 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: 0.63 (0.34), residues: 692 helix: 0.87 (0.26), residues: 398 sheet: -1.83 (0.61), residues: 76 loop : 0.76 (0.47), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 310 TYR 0.011 0.002 TYR A 194 PHE 0.020 0.002 PHE B 264 TRP 0.021 0.002 TRP B 98 HIS 0.007 0.002 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 ( 9718) covalent geometry : angle 0.59502 / 0.32 (13927) hydrogen bonds : bond 0.06254 / 3.86 ( 414) hydrogen bonds : angle 5.01143 / 3.63 ( 1057) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 TRP cc_start: 0.9513 (m100) cc_final: 0.9012 (m100) REVERT: A 242 HIS cc_start: 0.8430 (t-170) cc_final: 0.8095 (t-170) REVERT: B 74 HIS cc_start: 0.8459 (m170) cc_final: 0.8224 (m170) REVERT: B 124 LEU cc_start: 0.9879 (mt) cc_final: 0.9637 (mt) REVERT: B 162 ASP cc_start: 0.9449 (t0) cc_final: 0.9192 (t0) outliers start: 6 outliers final: 3 residues processed: 90 average time/residue: 0.0709 time to fit residues: 9.3924 Evaluate side-chains 72 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 215 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 71 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 79 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 72 optimal weight: 20.0000 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 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 = 0.3471 r_free = 0.3471 target = 0.053814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.037321 restraints weight = 73735.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.038344 restraints weight = 46790.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.038980 restraints weight = 34682.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.039431 restraints weight = 28957.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.039750 restraints weight = 25698.672| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 9718 Z= 0.279 Angle : 0.661 9.389 13927 Z= 0.362 Chirality : 0.038 0.217 1672 Planarity : 0.005 0.043 1153 Dihedral : 23.160 177.395 3356 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 27.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.44 % Allowed : 14.29 % Favored : 83.28 % 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: 0.49 (0.33), residues: 692 helix: 0.80 (0.26), residues: 408 sheet: -1.97 (0.63), residues: 68 loop : 0.52 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 310 TYR 0.024 0.003 TYR A 323 PHE 0.019 0.003 PHE A 264 TRP 0.013 0.002 TRP B 302 HIS 0.005 0.002 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.28 ( 9718) covalent geometry : angle 0.66106 / 0.36 (13927) hydrogen bonds : bond 0.07554 / 4.89 ( 414) hydrogen bonds : angle 5.15312 / 3.67 ( 1057) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9357 (mt-10) cc_final: 0.9053 (pt0) REVERT: A 242 HIS cc_start: 0.8616 (t-170) cc_final: 0.8364 (t70) REVERT: A 243 MET cc_start: 0.8416 (mmt) cc_final: 0.8142 (mmt) REVERT: B 74 HIS cc_start: 0.8519 (m170) cc_final: 0.8122 (m170) REVERT: B 96 LYS cc_start: 0.9520 (mttm) cc_final: 0.9029 (mmmm) REVERT: B 124 LEU cc_start: 0.9889 (mt) cc_final: 0.9657 (mt) REVERT: B 162 ASP cc_start: 0.9563 (t0) cc_final: 0.9287 (t0) outliers start: 15 outliers final: 10 residues processed: 77 average time/residue: 0.0692 time to fit residues: 8.0577 Evaluate side-chains 71 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 215 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 71 optimal weight: 30.0000 chunk 45 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 8 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 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 = 0.3537 r_free = 0.3537 target = 0.058314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.041696 restraints weight = 81437.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.042890 restraints weight = 51513.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.043644 restraints weight = 38662.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.044203 restraints weight = 32260.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.044495 restraints weight = 28687.448| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9718 Z= 0.165 Angle : 0.567 8.292 13927 Z= 0.305 Chirality : 0.036 0.229 1672 Planarity : 0.004 0.035 1153 Dihedral : 23.258 174.043 3356 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.60 % Allowed : 16.07 % Favored : 81.33 % 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: 0.61 (0.34), residues: 692 helix: 0.87 (0.26), residues: 410 sheet: -1.97 (0.59), residues: 76 loop : 0.77 (0.49), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 310 TYR 0.018 0.002 TYR A 323 PHE 0.018 0.002 PHE B 193 TRP 0.012 0.001 TRP A 98 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 ( 9718) covalent geometry : angle 0.56697 / 0.30 (13927) hydrogen bonds : bond 0.05781 / 3.65 ( 414) hydrogen bonds : angle 4.87399 / 3.47 ( 1057) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9350 (mt-10) cc_final: 0.9016 (pt0) REVERT: A 65 ASP cc_start: 0.9025 (p0) cc_final: 0.7919 (t0) REVERT: A 242 HIS cc_start: 0.8681 (t-170) cc_final: 0.8432 (t70) REVERT: A 243 MET cc_start: 0.8521 (mmt) cc_final: 0.8138 (mmt) REVERT: B 74 HIS cc_start: 0.8522 (m170) cc_final: 0.8249 (m170) REVERT: B 96 LYS cc_start: 0.9552 (mttm) cc_final: 0.9049 (mmmm) REVERT: B 193 PHE cc_start: 0.9657 (m-80) cc_final: 0.9453 (m-10) outliers start: 16 outliers final: 9 residues processed: 79 average time/residue: 0.0652 time to fit residues: 7.9655 Evaluate side-chains 71 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 215 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 63 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 50 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 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 = 0.3527 r_free = 0.3527 target = 0.056328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.039964 restraints weight = 72087.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.041095 restraints weight = 44902.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.041825 restraints weight = 32950.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.042311 restraints weight = 27217.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.042629 restraints weight = 24054.718| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9718 Z= 0.123 Angle : 0.556 9.567 13927 Z= 0.291 Chirality : 0.036 0.216 1672 Planarity : 0.004 0.033 1153 Dihedral : 23.197 174.585 3356 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.79 % Allowed : 16.88 % Favored : 81.33 % 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: 0.92 (0.34), residues: 692 helix: 1.17 (0.27), residues: 398 sheet: -2.02 (0.58), residues: 76 loop : 0.88 (0.48), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 310 TYR 0.022 0.002 TYR A 323 PHE 0.009 0.002 PHE A 264 TRP 0.014 0.001 TRP A 98 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 9718) covalent geometry : angle 0.55571 / 0.29 (13927) hydrogen bonds : bond 0.05401 / 3.37 ( 414) hydrogen bonds : angle 4.70423 / 3.32 ( 1057) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9367 (mt-10) cc_final: 0.9133 (mt-10) REVERT: A 65 ASP cc_start: 0.9036 (p0) cc_final: 0.7837 (t0) REVERT: A 157 TRP cc_start: 0.9359 (m100) cc_final: 0.8888 (m100) REVERT: A 242 HIS cc_start: 0.8756 (t-170) cc_final: 0.8487 (t70) REVERT: A 243 MET cc_start: 0.8451 (mmt) cc_final: 0.8117 (mmt) REVERT: A 294 TYR cc_start: 0.9353 (m-80) cc_final: 0.8989 (m-80) outliers start: 11 outliers final: 6 residues processed: 78 average time/residue: 0.0665 time to fit residues: 8.1382 Evaluate side-chains 73 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 215 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 71 optimal weight: 30.0000 chunk 52 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 73 optimal weight: 30.0000 chunk 7 optimal weight: 0.9980 chunk 74 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 77 optimal weight: 30.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 150 ASN ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.055118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.038979 restraints weight = 72888.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.040078 restraints weight = 45472.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.040766 restraints weight = 33505.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.041243 restraints weight = 27903.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.041561 restraints weight = 24565.622| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9718 Z= 0.154 Angle : 0.550 9.205 13927 Z= 0.293 Chirality : 0.035 0.205 1672 Planarity : 0.004 0.032 1153 Dihedral : 23.209 175.028 3356 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.60 % Allowed : 17.37 % Favored : 80.03 % 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: 1.00 (0.34), residues: 692 helix: 1.26 (0.27), residues: 398 sheet: -2.07 (0.57), residues: 76 loop : 0.91 (0.47), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 310 TYR 0.019 0.002 TYR A 323 PHE 0.021 0.002 PHE A 306 TRP 0.012 0.001 TRP A 98 HIS 0.007 0.001 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 ( 9718) covalent geometry : angle 0.54951 / 0.29 (13927) hydrogen bonds : bond 0.05598 / 3.54 ( 414) hydrogen bonds : angle 4.71377 / 3.34 ( 1057) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9378 (mt-10) cc_final: 0.9001 (pt0) REVERT: A 65 ASP cc_start: 0.9071 (p0) cc_final: 0.7851 (t0) REVERT: A 157 TRP cc_start: 0.9419 (m100) cc_final: 0.8989 (m100) REVERT: A 242 HIS cc_start: 0.8789 (t-170) cc_final: 0.8512 (t70) REVERT: A 243 MET cc_start: 0.8519 (mmt) cc_final: 0.8056 (mmt) REVERT: A 294 TYR cc_start: 0.9349 (m-80) cc_final: 0.8997 (m-80) REVERT: B 96 LYS cc_start: 0.9559 (mttm) cc_final: 0.9033 (mmtp) outliers start: 16 outliers final: 9 residues processed: 76 average time/residue: 0.0640 time to fit residues: 7.5839 Evaluate side-chains 70 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 215 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 150 ASN ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.056250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.039943 restraints weight = 70707.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.041094 restraints weight = 43851.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.041832 restraints weight = 32218.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.042361 restraints weight = 26423.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.042707 restraints weight = 23153.639| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 9718 Z= 0.118 Angle : 0.551 10.740 13927 Z= 0.287 Chirality : 0.035 0.190 1672 Planarity : 0.004 0.033 1153 Dihedral : 23.172 175.160 3356 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.62 % Allowed : 18.99 % Favored : 79.38 % 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: 1.01 (0.34), residues: 692 helix: 1.22 (0.27), residues: 398 sheet: -2.05 (0.57), residues: 76 loop : 1.01 (0.48), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 310 TYR 0.023 0.002 TYR A 323 PHE 0.016 0.002 PHE A 193 TRP 0.013 0.001 TRP B 98 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 9718) covalent geometry : angle 0.55128 / 0.29 (13927) hydrogen bonds : bond 0.05265 / 3.30 ( 414) hydrogen bonds : angle 4.62440 / 3.28 ( 1057) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9407 (mt-10) cc_final: 0.9055 (pt0) REVERT: A 65 ASP cc_start: 0.9058 (p0) cc_final: 0.7828 (t0) REVERT: A 157 TRP cc_start: 0.9392 (m100) cc_final: 0.8950 (m100) REVERT: A 242 HIS cc_start: 0.8847 (t-170) cc_final: 0.8494 (t-170) REVERT: A 243 MET cc_start: 0.8501 (mmt) cc_final: 0.8272 (mmm) REVERT: A 294 TYR cc_start: 0.9354 (m-80) cc_final: 0.9027 (m-80) REVERT: B 96 LYS cc_start: 0.9549 (mttm) cc_final: 0.9030 (mmtp) REVERT: B 110 MET cc_start: 0.8909 (ptp) cc_final: 0.8550 (ptt) REVERT: B 254 MET cc_start: 0.3526 (ptt) cc_final: 0.3266 (ptt) outliers start: 10 outliers final: 8 residues processed: 70 average time/residue: 0.0679 time to fit residues: 7.4897 Evaluate side-chains 71 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 215 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 32 optimal weight: 0.9990 chunk 69 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 77 optimal weight: 30.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.054656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.038597 restraints weight = 69432.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.039693 restraints weight = 42845.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.040355 restraints weight = 31520.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.040860 restraints weight = 26177.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.041188 restraints weight = 23062.012| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9718 Z= 0.159 Angle : 0.551 9.179 13927 Z= 0.295 Chirality : 0.035 0.201 1672 Planarity : 0.004 0.031 1153 Dihedral : 23.195 175.958 3356 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.60 % Allowed : 18.18 % Favored : 79.22 % 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: 1.08 (0.34), residues: 692 helix: 1.23 (0.26), residues: 400 sheet: -1.99 (0.58), residues: 76 loop : 1.11 (0.48), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 310 TYR 0.024 0.002 TYR A 323 PHE 0.035 0.002 PHE A 306 TRP 0.010 0.002 TRP B 98 HIS 0.002 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 ( 9718) covalent geometry : angle 0.55129 / 0.30 (13927) hydrogen bonds : bond 0.05647 / 3.58 ( 414) hydrogen bonds : angle 4.70275 / 3.32 ( 1057) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.9127 (p0) cc_final: 0.7890 (t0) REVERT: A 157 TRP cc_start: 0.9450 (m100) cc_final: 0.8975 (m100) REVERT: A 242 HIS cc_start: 0.8893 (t-170) cc_final: 0.8561 (t70) REVERT: A 243 MET cc_start: 0.8727 (mmt) cc_final: 0.8163 (mmt) REVERT: A 294 TYR cc_start: 0.9360 (m-80) cc_final: 0.9066 (m-80) REVERT: B 96 LYS cc_start: 0.9564 (mttm) cc_final: 0.9011 (mmtp) REVERT: B 110 MET cc_start: 0.9041 (ptp) cc_final: 0.8633 (ptt) REVERT: B 254 MET cc_start: 0.3776 (ptt) cc_final: 0.3354 (ptt) outliers start: 16 outliers final: 11 residues processed: 71 average time/residue: 0.0689 time to fit residues: 7.6784 Evaluate side-chains 67 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 215 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 20.0000 chunk 61 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 73 optimal weight: 30.0000 chunk 65 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 8 optimal weight: 0.0470 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 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 = 0.3492 r_free = 0.3492 target = 0.054427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.038023 restraints weight = 70020.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.039111 restraints weight = 42887.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.039803 restraints weight = 31516.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.040274 restraints weight = 25984.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.040551 restraints weight = 22935.378| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9718 Z= 0.137 Angle : 0.557 10.083 13927 Z= 0.294 Chirality : 0.035 0.194 1672 Planarity : 0.004 0.033 1153 Dihedral : 23.226 176.619 3356 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.92 % Allowed : 18.34 % Favored : 78.73 % 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: 1.10 (0.34), residues: 692 helix: 1.25 (0.26), residues: 400 sheet: -1.99 (0.57), residues: 76 loop : 1.12 (0.48), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 181 TYR 0.029 0.002 TYR A 323 PHE 0.014 0.002 PHE A 193 TRP 0.011 0.001 TRP B 98 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 ( 9718) covalent geometry : angle 0.55733 / 0.29 (13927) hydrogen bonds : bond 0.05301 / 3.33 ( 414) hydrogen bonds : angle 4.67884 / 3.28 ( 1057) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.9073 (p0) cc_final: 0.7898 (t0) REVERT: A 157 TRP cc_start: 0.9410 (m100) cc_final: 0.8982 (m100) REVERT: A 242 HIS cc_start: 0.8918 (t-170) cc_final: 0.8575 (t70) REVERT: A 243 MET cc_start: 0.8665 (mmt) cc_final: 0.8092 (mmt) REVERT: A 294 TYR cc_start: 0.9352 (m-80) cc_final: 0.9087 (m-80) REVERT: B 95 VAL cc_start: 0.9508 (OUTLIER) cc_final: 0.9190 (p) REVERT: B 96 LYS cc_start: 0.9574 (mttm) cc_final: 0.9074 (mmmm) REVERT: B 254 MET cc_start: 0.3881 (ptt) cc_final: 0.3475 (ptt) outliers start: 18 outliers final: 11 residues processed: 75 average time/residue: 0.0656 time to fit residues: 7.4235 Evaluate side-chains 72 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 215 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 74 optimal weight: 20.0000 chunk 46 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 77 optimal weight: 30.0000 chunk 41 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.054755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.037855 restraints weight = 72993.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.038956 restraints weight = 45368.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.039659 restraints weight = 33501.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.040104 restraints weight = 27739.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.040429 restraints weight = 24752.224| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9718 Z= 0.131 Angle : 0.562 9.580 13927 Z= 0.294 Chirality : 0.035 0.190 1672 Planarity : 0.004 0.034 1153 Dihedral : 23.194 177.779 3356 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.11 % Allowed : 18.99 % Favored : 78.90 % 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: 1.10 (0.34), residues: 692 helix: 1.23 (0.26), residues: 400 sheet: -1.92 (0.58), residues: 76 loop : 1.12 (0.48), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 310 TYR 0.031 0.002 TYR A 323 PHE 0.032 0.002 PHE A 306 TRP 0.031 0.002 TRP B 98 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 9718) covalent geometry : angle 0.56181 / 0.29 (13927) hydrogen bonds : bond 0.05253 / 3.30 ( 414) hydrogen bonds : angle 4.62784 / 3.26 ( 1057) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.9061 (p0) cc_final: 0.7892 (t0) REVERT: A 157 TRP cc_start: 0.9379 (m100) cc_final: 0.8941 (m100) REVERT: A 242 HIS cc_start: 0.8948 (t-170) cc_final: 0.8568 (t-170) REVERT: A 243 MET cc_start: 0.8647 (mmt) cc_final: 0.8337 (mmm) REVERT: A 294 TYR cc_start: 0.9343 (m-80) cc_final: 0.9119 (m-80) REVERT: B 95 VAL cc_start: 0.9517 (OUTLIER) cc_final: 0.9216 (p) REVERT: B 96 LYS cc_start: 0.9586 (mttm) cc_final: 0.9101 (mmmm) REVERT: B 110 MET cc_start: 0.8922 (ptp) cc_final: 0.8034 (pmm) REVERT: B 254 MET cc_start: 0.3928 (ptt) cc_final: 0.3584 (ptt) outliers start: 13 outliers final: 12 residues processed: 66 average time/residue: 0.0623 time to fit residues: 6.3326 Evaluate side-chains 72 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 215 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 71 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 72 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 78 optimal weight: 50.0000 chunk 57 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 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 = 0.3498 r_free = 0.3498 target = 0.054497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.037551 restraints weight = 72349.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.038643 restraints weight = 45428.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.039376 restraints weight = 33788.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.039861 restraints weight = 27916.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.040135 restraints weight = 24670.564| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9718 Z= 0.137 Angle : 0.565 12.680 13927 Z= 0.295 Chirality : 0.034 0.191 1672 Planarity : 0.004 0.034 1153 Dihedral : 23.185 179.197 3356 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.27 % Allowed : 19.32 % Favored : 78.41 % 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: 1.12 (0.34), residues: 692 helix: 1.24 (0.26), residues: 400 sheet: -1.89 (0.59), residues: 76 loop : 1.13 (0.48), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 310 TYR 0.032 0.002 TYR A 323 PHE 0.018 0.002 PHE A 193 TRP 0.022 0.001 TRP B 98 HIS 0.003 0.001 HIS B 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 ( 9718) covalent geometry : angle 0.56538 / 0.29 (13927) hydrogen bonds : bond 0.05290 / 3.33 ( 414) hydrogen bonds : angle 4.63640 / 3.26 ( 1057) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1630.41 seconds wall clock time: 28 minutes 56.63 seconds (1736.63 seconds total)