Starting phenix.real_space_refine on Thu Jul 2 15:13:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zmj_60249/07_2026/8zmj_60249.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zmj_60249/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zmj_60249/07_2026/8zmj_60249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zmj_60249/07_2026/8zmj_60249.map" model { file = "/net/cci-nas-00/data/ceres_data/8zmj_60249/07_2026/8zmj_60249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zmj_60249/07_2026/8zmj_60249.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.24, per 1000 atoms: 0.24 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: 0.83 Conformation dependent library (CDL) restraints added in 219.5 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: 1.43 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: 1.72 Time building geometry restraints manager: 1.11 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=" 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 bond pdb=" N GLU B 266 " pdb=" CA GLU B 266 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.32e-02 5.74e+03 6.79e+00 ... (remaining 9713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 13539 1.95 - 3.90: 336 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: 1480 0.062 - 0.125: 127 0.125 - 0.187: 45 0.187 - 0.250: 16 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: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.160 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.520 ------------------------------------------------------------------------------- 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= 0.263 Angle : 0.682 9.739 13927 Z= 0.484 Chirality : 0.050 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 0.00411 / 0.26 ( 9718) covalent geometry : angle 0.68182 / 0.48 (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 : 0.284 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: 0.0969 time to fit residues: 16.4615 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 : 0.176 ------------------------------------------------------------------------------- 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: 10.0000 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 248 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.058954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.042358 restraints weight = 68639.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.043481 restraints weight = 42793.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.044201 restraints weight = 31649.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.044734 restraints weight = 26120.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.045049 restraints weight = 22781.493| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9718 Z= 0.150 Angle : 0.582 8.096 13927 Z= 0.318 Chirality : 0.037 0.251 1672 Planarity : 0.004 0.032 1153 Dihedral : 23.010 162.681 3356 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.97 % Allowed : 10.88 % Favored : 88.15 % 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: 0.86 (0.26), residues: 400 sheet: -1.82 (0.61), residues: 76 loop : 0.85 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 360 TYR 0.011 0.002 TYR A 194 PHE 0.017 0.002 PHE B 264 TRP 0.022 0.002 TRP B 98 HIS 0.007 0.002 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 ( 9718) covalent geometry : angle 0.58239 / 0.32 (13927) hydrogen bonds : bond 0.06197 / 3.83 ( 414) hydrogen bonds : angle 5.01696 / 3.64 ( 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 89 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 TRP cc_start: 0.9518 (m100) cc_final: 0.9025 (m100) REVERT: A 242 HIS cc_start: 0.8426 (t-170) cc_final: 0.8087 (t-170) REVERT: B 74 HIS cc_start: 0.8463 (m170) cc_final: 0.8136 (m170) REVERT: B 124 LEU cc_start: 0.9878 (mt) cc_final: 0.9637 (mt) REVERT: B 162 ASP cc_start: 0.9451 (t0) cc_final: 0.9186 (t0) outliers start: 6 outliers final: 3 residues processed: 88 average time/residue: 0.0767 time to fit residues: 9.9776 Evaluate side-chains 71 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 123 TYR 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: 10.0000 chunk 21 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 overall best weight: 5.1986 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.052693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.036768 restraints weight = 74614.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.037752 restraints weight = 46904.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.038367 restraints weight = 34966.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.038820 restraints weight = 29222.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.039099 restraints weight = 25911.989| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 9718 Z= 0.332 Angle : 0.716 9.372 13927 Z= 0.397 Chirality : 0.041 0.258 1672 Planarity : 0.006 0.055 1153 Dihedral : 23.410 178.121 3356 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 31.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.76 % Allowed : 14.77 % Favored : 82.47 % 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: 0.19 (0.33), residues: 692 helix: 0.63 (0.25), residues: 404 sheet: -2.08 (0.63), residues: 68 loop : 0.22 (0.45), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 310 TYR 0.019 0.003 TYR A 323 PHE 0.035 0.004 PHE B 264 TRP 0.017 0.003 TRP B 302 HIS 0.007 0.002 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00649 / 0.33 ( 9718) covalent geometry : angle 0.71648 / 0.40 (13927) hydrogen bonds : bond 0.08847 / 5.83 ( 414) hydrogen bonds : angle 5.32991 / 3.79 ( 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: 17 poor density : 64 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9355 (mt-10) cc_final: 0.9051 (pt0) REVERT: A 242 HIS cc_start: 0.8621 (t-170) cc_final: 0.8405 (t70) REVERT: B 74 HIS cc_start: 0.8557 (m170) cc_final: 0.8185 (m170) REVERT: B 162 ASP cc_start: 0.9586 (t0) cc_final: 0.9323 (t0) REVERT: B 193 PHE cc_start: 0.9660 (m-80) cc_final: 0.9361 (m-80) REVERT: B 197 MET cc_start: 0.9200 (mtm) cc_final: 0.8606 (mtt) outliers start: 17 outliers final: 12 residues processed: 78 average time/residue: 0.0821 time to fit residues: 9.6137 Evaluate side-chains 68 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 209 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 Chi-restraints excluded: chain B residue 239 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.0980 chunk 20 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 71 optimal weight: 20.0000 chunk 45 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 chunk 52 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.055861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.039328 restraints weight = 70771.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.040485 restraints weight = 43272.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.041238 restraints weight = 31660.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.041756 restraints weight = 26016.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.042097 restraints weight = 22779.973| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9718 Z= 0.130 Angle : 0.594 12.336 13927 Z= 0.310 Chirality : 0.037 0.247 1672 Planarity : 0.004 0.034 1153 Dihedral : 23.391 171.997 3356 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.95 % Allowed : 16.56 % Favored : 81.49 % 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: 0.53 (0.34), residues: 692 helix: 0.79 (0.26), residues: 410 sheet: -2.00 (0.60), residues: 76 loop : 0.79 (0.49), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 232 TYR 0.019 0.002 TYR A 226 PHE 0.010 0.002 PHE A 264 TRP 0.015 0.001 TRP A 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 0.59390 / 0.31 (13927) hydrogen bonds : bond 0.05443 / 3.39 ( 414) hydrogen bonds : angle 4.81481 / 3.44 ( 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 85 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9359 (mt-10) cc_final: 0.9000 (pt0) REVERT: A 65 ASP cc_start: 0.9093 (p0) cc_final: 0.7923 (t0) REVERT: A 157 TRP cc_start: 0.9484 (m100) cc_final: 0.9158 (m100) REVERT: A 242 HIS cc_start: 0.8640 (t-170) cc_final: 0.8371 (t70) REVERT: A 243 MET cc_start: 0.8468 (mmm) cc_final: 0.8100 (mmt) REVERT: A 294 TYR cc_start: 0.9341 (m-80) cc_final: 0.8981 (m-80) REVERT: B 74 HIS cc_start: 0.8457 (m170) cc_final: 0.8092 (m170) REVERT: B 96 LYS cc_start: 0.9547 (mttm) cc_final: 0.9028 (mmmm) REVERT: B 110 MET cc_start: 0.8746 (ptp) cc_final: 0.8432 (ptt) REVERT: B 162 ASP cc_start: 0.9573 (t0) cc_final: 0.9370 (t0) REVERT: B 193 PHE cc_start: 0.9659 (m-80) cc_final: 0.9296 (m-80) REVERT: B 197 MET cc_start: 0.9126 (mtm) cc_final: 0.8468 (mtt) outliers start: 12 outliers final: 4 residues processed: 84 average time/residue: 0.0673 time to fit residues: 8.8718 Evaluate side-chains 74 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 340 LEU 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: 4.9990 chunk 30 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.054538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.038747 restraints weight = 71733.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.039855 restraints weight = 44055.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.040545 restraints weight = 32355.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.041019 restraints weight = 26838.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.041329 restraints weight = 23620.843| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9718 Z= 0.182 Angle : 0.587 10.223 13927 Z= 0.311 Chirality : 0.036 0.230 1672 Planarity : 0.004 0.033 1153 Dihedral : 23.388 173.880 3356 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 22.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.27 % Allowed : 16.88 % Favored : 80.84 % 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: 0.54 (0.34), residues: 692 helix: 0.81 (0.26), residues: 410 sheet: -2.06 (0.58), residues: 76 loop : 0.80 (0.49), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 310 TYR 0.018 0.002 TYR A 323 PHE 0.020 0.002 PHE A 306 TRP 0.012 0.001 TRP A 98 HIS 0.004 0.001 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 ( 9718) covalent geometry : angle 0.58685 / 0.31 (13927) hydrogen bonds : bond 0.06007 / 3.82 ( 414) hydrogen bonds : angle 4.87759 / 3.46 ( 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 77 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9369 (mt-10) cc_final: 0.8990 (pt0) REVERT: A 242 HIS cc_start: 0.8725 (t-170) cc_final: 0.8476 (t70) REVERT: A 294 TYR cc_start: 0.9381 (m-80) cc_final: 0.8976 (m-80) REVERT: B 96 LYS cc_start: 0.9571 (mttm) cc_final: 0.9050 (mmmm) REVERT: B 162 ASP cc_start: 0.9621 (t0) cc_final: 0.9402 (t0) outliers start: 14 outliers final: 8 residues processed: 75 average time/residue: 0.0743 time to fit residues: 8.6629 Evaluate side-chains 69 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 71 optimal weight: 20.0000 chunk 52 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 chunk 7 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.053706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.037578 restraints weight = 71554.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.038651 restraints weight = 43912.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.039334 restraints weight = 32231.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.039783 restraints weight = 26619.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.040095 restraints weight = 23498.371| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9718 Z= 0.172 Angle : 0.567 8.585 13927 Z= 0.303 Chirality : 0.036 0.228 1672 Planarity : 0.004 0.032 1153 Dihedral : 23.442 173.623 3356 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 22.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.44 % Allowed : 18.83 % 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: 0.82 (0.34), residues: 692 helix: 1.09 (0.26), residues: 398 sheet: -2.09 (0.57), residues: 76 loop : 0.84 (0.47), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 310 TYR 0.020 0.002 TYR A 323 PHE 0.021 0.002 PHE B 193 TRP 0.012 0.002 TRP A 98 HIS 0.007 0.001 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 ( 9718) covalent geometry : angle 0.56705 / 0.30 (13927) hydrogen bonds : bond 0.05721 / 3.63 ( 414) hydrogen bonds : angle 4.80986 / 3.41 ( 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 75 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9378 (mt-10) cc_final: 0.8990 (pt0) REVERT: A 157 TRP cc_start: 0.9414 (m100) cc_final: 0.9007 (m100) REVERT: A 242 HIS cc_start: 0.8763 (t-170) cc_final: 0.8525 (t70) REVERT: A 294 TYR cc_start: 0.9370 (m-80) cc_final: 0.9004 (m-80) REVERT: B 96 LYS cc_start: 0.9583 (mttm) cc_final: 0.9072 (mmmm) REVERT: B 110 MET cc_start: 0.8853 (ptp) cc_final: 0.8513 (ptt) REVERT: B 162 ASP cc_start: 0.9652 (t0) cc_final: 0.9428 (t0) outliers start: 15 outliers final: 11 residues processed: 70 average time/residue: 0.0733 time to fit residues: 7.9217 Evaluate side-chains 70 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 178 ILE 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 73 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.055726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.038569 restraints weight = 71533.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.039671 restraints weight = 44696.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.040435 restraints weight = 33235.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.040965 restraints weight = 27314.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.041287 restraints weight = 23982.314| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9718 Z= 0.115 Angle : 0.558 9.902 13927 Z= 0.291 Chirality : 0.036 0.230 1672 Planarity : 0.004 0.034 1153 Dihedral : 23.339 172.929 3356 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.95 % Allowed : 18.67 % 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: 0.99 (0.34), residues: 692 helix: 1.19 (0.27), residues: 400 sheet: -1.92 (0.57), residues: 76 loop : 0.96 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 224 TYR 0.024 0.002 TYR A 323 PHE 0.026 0.002 PHE A 306 TRP 0.015 0.002 TRP B 98 HIS 0.002 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 9718) covalent geometry : angle 0.55792 / 0.29 (13927) hydrogen bonds : bond 0.05225 / 3.27 ( 414) hydrogen bonds : angle 4.59488 / 3.27 ( 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 80 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9412 (mt-10) cc_final: 0.9068 (pt0) REVERT: A 65 ASP cc_start: 0.9099 (p0) cc_final: 0.7805 (t0) REVERT: A 157 TRP cc_start: 0.9383 (m100) cc_final: 0.9014 (m100) REVERT: A 242 HIS cc_start: 0.8776 (t-170) cc_final: 0.8516 (t70) REVERT: A 243 MET cc_start: 0.8234 (mmm) cc_final: 0.7971 (mmm) REVERT: A 294 TYR cc_start: 0.9375 (m-80) cc_final: 0.9093 (m-80) REVERT: B 96 LYS cc_start: 0.9565 (mttm) cc_final: 0.9044 (mmmm) REVERT: B 110 MET cc_start: 0.8800 (ptp) cc_final: 0.8506 (ptt) REVERT: B 162 ASP cc_start: 0.9658 (t0) cc_final: 0.9402 (t0) outliers start: 12 outliers final: 8 residues processed: 74 average time/residue: 0.0756 time to fit residues: 8.7174 Evaluate side-chains 72 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.161 ------------------------------------------------------------------------------- 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 340 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 73 MET 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: 0.6980 chunk 69 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.055049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.038207 restraints weight = 71942.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.039298 restraints weight = 44624.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.039994 restraints weight = 32980.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.040487 restraints weight = 27188.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.040766 restraints weight = 23984.419| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9718 Z= 0.126 Angle : 0.547 10.532 13927 Z= 0.289 Chirality : 0.035 0.234 1672 Planarity : 0.004 0.033 1153 Dihedral : 23.274 173.350 3356 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.27 % Allowed : 19.16 % Favored : 78.57 % 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: 1.06 (0.34), residues: 692 helix: 1.23 (0.27), residues: 398 sheet: -1.80 (0.58), residues: 76 loop : 0.98 (0.47), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 310 TYR 0.027 0.002 TYR A 323 PHE 0.018 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 0.00264 / 0.13 ( 9718) covalent geometry : angle 0.54685 / 0.29 (13927) hydrogen bonds : bond 0.05280 / 3.30 ( 414) hydrogen bonds : angle 4.62306 / 3.26 ( 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 79 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9419 (mt-10) cc_final: 0.9094 (pt0) REVERT: A 65 ASP cc_start: 0.9133 (p0) cc_final: 0.7838 (t0) REVERT: A 157 TRP cc_start: 0.9373 (m100) cc_final: 0.8967 (m100) REVERT: A 242 HIS cc_start: 0.8809 (t-170) cc_final: 0.8542 (t70) REVERT: A 243 MET cc_start: 0.8263 (mmm) cc_final: 0.8036 (mmm) REVERT: A 294 TYR cc_start: 0.9373 (m-80) cc_final: 0.9106 (m-80) REVERT: B 95 VAL cc_start: 0.9478 (OUTLIER) cc_final: 0.9181 (p) REVERT: B 96 LYS cc_start: 0.9558 (mttm) cc_final: 0.9042 (mmmm) REVERT: B 110 MET cc_start: 0.8815 (ptp) cc_final: 0.8551 (ptt) REVERT: B 162 ASP cc_start: 0.9673 (t0) cc_final: 0.9406 (t0) outliers start: 14 outliers final: 10 residues processed: 75 average time/residue: 0.0713 time to fit residues: 8.3449 Evaluate side-chains 76 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 197 MET Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 95 VAL 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: 0.9980 chunk 11 optimal weight: 0.5980 chunk 73 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- 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 241 HIS ** 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 = 0.3478 r_free = 0.3478 target = 0.053826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.037468 restraints weight = 70926.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.038557 restraints weight = 43969.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.039259 restraints weight = 32504.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.039735 restraints weight = 26799.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.040023 restraints weight = 23667.051| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3172 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= 0.163 Angle : 0.564 9.977 13927 Z= 0.300 Chirality : 0.036 0.225 1672 Planarity : 0.004 0.033 1153 Dihedral : 23.336 173.143 3356 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.60 % Allowed : 19.64 % Favored : 77.76 % 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: 0.95 (0.33), residues: 692 helix: 1.12 (0.26), residues: 400 sheet: -1.80 (0.59), residues: 76 loop : 0.97 (0.48), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 310 TYR 0.020 0.002 TYR A 323 PHE 0.018 0.002 PHE A 193 TRP 0.009 0.001 TRP B 98 HIS 0.003 0.001 HIS B 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 ( 9718) covalent geometry : angle 0.56436 / 0.30 (13927) hydrogen bonds : bond 0.05519 / 3.49 ( 414) hydrogen bonds : angle 4.73308 / 3.30 ( 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 76 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 TRP cc_start: 0.9440 (m100) cc_final: 0.9090 (m100) REVERT: A 242 HIS cc_start: 0.8873 (t-170) cc_final: 0.8603 (t70) REVERT: A 243 MET cc_start: 0.8327 (mmm) cc_final: 0.8118 (mmm) REVERT: A 294 TYR cc_start: 0.9394 (m-80) cc_final: 0.9136 (m-80) REVERT: B 95 VAL cc_start: 0.9516 (OUTLIER) cc_final: 0.9195 (p) REVERT: B 96 LYS cc_start: 0.9596 (mttm) cc_final: 0.9096 (mmmm) REVERT: B 162 ASP cc_start: 0.9697 (t0) cc_final: 0.9441 (t0) outliers start: 16 outliers final: 11 residues processed: 69 average time/residue: 0.0793 time to fit residues: 8.3132 Evaluate side-chains 70 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 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 73 MET Chi-restraints excluded: chain B residue 95 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 74 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 77 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 241 HIS ** 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 = 0.3502 r_free = 0.3502 target = 0.054709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.037911 restraints weight = 72691.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.039028 restraints weight = 45317.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.039757 restraints weight = 33536.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.040264 restraints weight = 27698.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.040549 restraints weight = 24389.953| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3228 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= 0.124 Angle : 0.571 11.399 13927 Z= 0.296 Chirality : 0.036 0.224 1672 Planarity : 0.004 0.035 1153 Dihedral : 23.331 172.710 3356 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.60 % Allowed : 19.64 % Favored : 77.76 % 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: 1.04 (0.34), residues: 692 helix: 1.20 (0.26), residues: 398 sheet: -1.78 (0.60), 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 0.033 0.002 TYR A 323 PHE 0.020 0.002 PHE A 193 TRP 0.013 0.001 TRP B 98 HIS 0.002 0.001 HIS B 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 9718) covalent geometry : angle 0.57103 / 0.30 (13927) hydrogen bonds : bond 0.05164 / 3.24 ( 414) hydrogen bonds : angle 4.60588 / 3.24 ( 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 82 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9431 (mt-10) cc_final: 0.9092 (pt0) REVERT: A 65 ASP cc_start: 0.9073 (p0) cc_final: 0.7770 (t0) REVERT: A 157 TRP cc_start: 0.9377 (m100) cc_final: 0.8995 (m100) REVERT: A 242 HIS cc_start: 0.8866 (t-170) cc_final: 0.8616 (t70) REVERT: A 243 MET cc_start: 0.8481 (mmm) cc_final: 0.8235 (mmm) REVERT: A 294 TYR cc_start: 0.9392 (m-80) cc_final: 0.9156 (m-80) REVERT: B 95 VAL cc_start: 0.9521 (OUTLIER) cc_final: 0.9209 (p) REVERT: B 96 LYS cc_start: 0.9593 (mttm) cc_final: 0.9100 (mmmm) REVERT: B 110 MET cc_start: 0.8823 (ptp) cc_final: 0.7846 (pmm) REVERT: B 162 ASP cc_start: 0.9699 (t0) cc_final: 0.9417 (t0) outliers start: 16 outliers final: 12 residues processed: 75 average time/residue: 0.0776 time to fit residues: 8.9524 Evaluate side-chains 76 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 73 MET Chi-restraints excluded: chain B residue 95 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 71 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 78 optimal weight: 40.0000 chunk 57 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3506 r_free = 0.3506 target = 0.054960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.038320 restraints weight = 71372.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.039431 restraints weight = 44383.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.040119 restraints weight = 32678.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.040542 restraints weight = 27033.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.040892 restraints weight = 24096.824| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9718 Z= 0.119 Angle : 0.556 10.656 13927 Z= 0.290 Chirality : 0.035 0.223 1672 Planarity : 0.004 0.035 1153 Dihedral : 23.256 173.021 3356 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.76 % Allowed : 19.16 % Favored : 78.08 % 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: 1.06 (0.34), residues: 692 helix: 1.22 (0.27), residues: 398 sheet: -1.85 (0.60), residues: 76 loop : 1.04 (0.48), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 310 TYR 0.030 0.002 TYR A 323 PHE 0.020 0.002 PHE B 193 TRP 0.039 0.002 TRP B 98 HIS 0.002 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 9718) covalent geometry : angle 0.55612 / 0.29 (13927) hydrogen bonds : bond 0.05154 / 3.23 ( 414) hydrogen bonds : angle 4.56863 / 3.22 ( 1057) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1910.61 seconds wall clock time: 33 minutes 56.72 seconds (2036.72 seconds total)