Starting phenix.real_space_refine on Wed Sep 17 14:20:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zmj_60249/09_2025/8zmj_60249.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zmj_60249/09_2025/8zmj_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_60249/09_2025/8zmj_60249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zmj_60249/09_2025/8zmj_60249.map" model { file = "/net/cci-nas-00/data/ceres_data/8zmj_60249/09_2025/8zmj_60249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zmj_60249/09_2025/8zmj_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-2.0-5805/lib/python3.9/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: 2.08, per 1000 atoms: 0.23 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: 0.88 Conformation dependent library (CDL) restraints added in 149.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 1.22 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: 1.92 Time building geometry restraints manager: 1.08 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=" 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=" 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 angle pdb=" N GLU B 68 " pdb=" CA GLU B 68 " pdb=" C GLU B 68 " ideal model delta sigma weight residual 109.24 103.49 5.75 1.39e+00 5.18e-01 1.71e+01 angle pdb=" CA ALA B 100 " pdb=" C ALA B 100 " pdb=" O ALA B 100 " ideal model delta sigma weight residual 122.63 117.56 5.07 1.29e+00 6.01e-01 1.54e+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: 3.650 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.690 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 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= 0.241 Angle : 0.682 9.739 13927 Z= 0.405 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 aren 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 covalent geometry : bond 0.00411 ( 9718) covalent geometry : angle 0.68175 (13927) hydrogen bonds : bond 0.14274 ( 414) hydrogen bonds : angle 6.47670 ( 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 : 0.253 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: 0.0949 time to fit residues: 15.8851 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: 9.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 B 248 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.058617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.042225 restraints weight = 68563.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.043347 restraints weight = 42793.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.044061 restraints weight = 31379.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.044575 restraints weight = 25757.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.044908 restraints weight = 22592.367| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1611 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= 0.148 Angle : 0.616 8.987 13927 Z= 0.307 Chirality : 0.035 0.182 1672 Planarity : 0.004 0.033 1153 Dihedral : 22.958 175.048 3356 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.97 % Allowed : 10.06 % Favored : 88.96 % 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 aren not related in a simple way. whole: 0.88 (0.34), residues: 692 helix: 1.03 (0.26), residues: 400 sheet: -1.68 (0.63), residues: 76 loop : 0.93 (0.48), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 360 TYR 0.013 0.002 TYR B 280 PHE 0.013 0.002 PHE A 264 TRP 0.022 0.002 TRP B 98 HIS 0.006 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9718) covalent geometry : angle 0.61562 (13927) hydrogen bonds : bond 0.05255 ( 414) hydrogen bonds : angle 4.84037 ( 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 97 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9372 (mt-10) cc_final: 0.9123 (pt0) REVERT: A 65 ASP cc_start: 0.9018 (p0) cc_final: 0.8008 (t0) REVERT: A 157 TRP cc_start: 0.9526 (m100) cc_final: 0.8913 (m100) REVERT: B 74 HIS cc_start: 0.8416 (m170) cc_final: 0.8047 (m-70) REVERT: B 96 LYS cc_start: 0.9595 (mttm) cc_final: 0.9092 (mmmm) REVERT: B 124 LEU cc_start: 0.9870 (mt) cc_final: 0.9643 (mt) REVERT: B 162 ASP cc_start: 0.9488 (t0) cc_final: 0.9213 (t0) outliers start: 6 outliers final: 4 residues processed: 96 average time/residue: 0.0847 time to fit residues: 11.8402 Evaluate side-chains 66 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 71 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 25 optimal weight: 0.0070 chunk 6 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 overall best weight: 3.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3445 r_free = 0.3445 target = 0.052401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.036228 restraints weight = 73496.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.037266 restraints weight = 46122.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.037941 restraints weight = 34308.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.038398 restraints weight = 28444.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.038666 restraints weight = 25180.222| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9718 Z= 0.267 Angle : 0.711 9.435 13927 Z= 0.357 Chirality : 0.037 0.213 1672 Planarity : 0.005 0.034 1153 Dihedral : 23.473 179.450 3356 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 28.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.76 % Allowed : 13.80 % Favored : 83.44 % 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 aren not related in a simple way. whole: 0.29 (0.33), residues: 692 helix: 0.65 (0.26), residues: 418 sheet: -1.96 (0.68), residues: 64 loop : 0.30 (0.46), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 310 TYR 0.022 0.003 TYR A 323 PHE 0.025 0.003 PHE A 264 TRP 0.026 0.002 TRP B 128 HIS 0.019 0.003 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 9718) covalent geometry : angle 0.71104 (13927) hydrogen bonds : bond 0.06970 ( 414) hydrogen bonds : angle 4.86087 ( 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 84 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9372 (mt-10) cc_final: 0.9110 (pt0) REVERT: A 242 HIS cc_start: 0.8883 (t-170) cc_final: 0.8395 (t70) REVERT: A 243 MET cc_start: 0.8383 (mmt) cc_final: 0.7650 (mmt) REVERT: A 294 TYR cc_start: 0.9282 (m-80) cc_final: 0.8972 (m-80) REVERT: A 306 PHE cc_start: 0.9479 (t80) cc_final: 0.9266 (t80) REVERT: B 74 HIS cc_start: 0.8330 (m170) cc_final: 0.8084 (m-70) REVERT: B 124 LEU cc_start: 0.9895 (mt) cc_final: 0.9690 (mt) REVERT: B 162 ASP cc_start: 0.9659 (t0) cc_final: 0.9450 (t0) REVERT: B 193 PHE cc_start: 0.9714 (m-80) cc_final: 0.9391 (m-80) REVERT: B 197 MET cc_start: 0.9126 (mtm) cc_final: 0.8464 (mtt) outliers start: 17 outliers final: 7 residues processed: 79 average time/residue: 0.0726 time to fit residues: 8.6856 Evaluate side-chains 69 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 239 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.054805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.038231 restraints weight = 70297.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.039322 restraints weight = 43260.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.040024 restraints weight = 31757.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.040530 restraints weight = 26203.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.040826 restraints weight = 22904.630| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9718 Z= 0.130 Angle : 0.601 8.664 13927 Z= 0.292 Chirality : 0.034 0.164 1672 Planarity : 0.004 0.033 1153 Dihedral : 23.278 176.760 3356 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.79 % Allowed : 14.94 % 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 aren not related in a simple way. whole: 0.81 (0.34), residues: 692 helix: 1.07 (0.26), residues: 404 sheet: -1.75 (0.65), residues: 72 loop : 0.64 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 310 TYR 0.015 0.002 TYR A 323 PHE 0.013 0.001 PHE A 264 TRP 0.022 0.001 TRP B 128 HIS 0.004 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9718) covalent geometry : angle 0.60055 (13927) hydrogen bonds : bond 0.04834 ( 414) hydrogen bonds : angle 4.51437 ( 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 76 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9409 (mt-10) cc_final: 0.9101 (pt0) REVERT: A 65 ASP cc_start: 0.9048 (p0) cc_final: 0.8006 (t0) REVERT: A 157 TRP cc_start: 0.9469 (m100) cc_final: 0.8984 (m100) REVERT: A 242 HIS cc_start: 0.8850 (t-170) cc_final: 0.8429 (t-170) REVERT: A 294 TYR cc_start: 0.9361 (m-80) cc_final: 0.9106 (m-80) REVERT: B 110 MET cc_start: 0.8857 (ptp) cc_final: 0.8473 (ptt) REVERT: B 162 ASP cc_start: 0.9667 (t0) cc_final: 0.9423 (t0) REVERT: B 193 PHE cc_start: 0.9725 (m-80) cc_final: 0.9371 (m-80) REVERT: B 197 MET cc_start: 0.9139 (mtm) cc_final: 0.8437 (mtt) outliers start: 11 outliers final: 6 residues processed: 75 average time/residue: 0.0648 time to fit residues: 7.4653 Evaluate side-chains 66 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 12 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3478 r_free = 0.3478 target = 0.053858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.037647 restraints weight = 70047.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.038703 restraints weight = 43046.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.039364 restraints weight = 31570.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.039825 restraints weight = 26010.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.040115 restraints weight = 22884.752| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9718 Z= 0.140 Angle : 0.605 8.206 13927 Z= 0.292 Chirality : 0.034 0.160 1672 Planarity : 0.004 0.035 1153 Dihedral : 23.206 178.568 3356 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.11 % Allowed : 16.88 % Favored : 81.01 % 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 aren not related in a simple way. whole: 0.94 (0.34), residues: 692 helix: 1.18 (0.26), residues: 404 sheet: -1.87 (0.64), residues: 72 loop : 0.77 (0.48), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 310 TYR 0.013 0.002 TYR B 123 PHE 0.023 0.002 PHE A 306 TRP 0.024 0.002 TRP B 128 HIS 0.002 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9718) covalent geometry : angle 0.60460 (13927) hydrogen bonds : bond 0.04930 ( 414) hydrogen bonds : angle 4.57237 ( 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 78 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9405 (mt-10) cc_final: 0.9131 (pt0) REVERT: A 65 ASP cc_start: 0.9108 (p0) cc_final: 0.8022 (t0) REVERT: A 157 TRP cc_start: 0.9448 (m100) cc_final: 0.9098 (m100) REVERT: A 242 HIS cc_start: 0.8835 (t-170) cc_final: 0.8350 (t-170) REVERT: A 294 TYR cc_start: 0.9394 (m-80) cc_final: 0.9177 (m-80) REVERT: B 96 LYS cc_start: 0.9449 (mttm) cc_final: 0.8934 (mmtp) REVERT: B 162 ASP cc_start: 0.9703 (t0) cc_final: 0.9440 (t0) outliers start: 13 outliers final: 7 residues processed: 73 average time/residue: 0.0678 time to fit residues: 7.6608 Evaluate side-chains 67 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 197 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 123 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 71 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3457 r_free = 0.3457 target = 0.052944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.036831 restraints weight = 71002.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.037851 restraints weight = 43452.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.038501 restraints weight = 31865.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.038957 restraints weight = 26264.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.039249 restraints weight = 23091.462| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9718 Z= 0.162 Angle : 0.617 9.218 13927 Z= 0.299 Chirality : 0.034 0.180 1672 Planarity : 0.004 0.038 1153 Dihedral : 23.273 177.575 3356 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.60 % Allowed : 17.86 % Favored : 79.55 % 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 aren not related in a simple way. whole: 0.99 (0.34), residues: 692 helix: 1.25 (0.26), residues: 404 sheet: -1.99 (0.62), residues: 72 loop : 0.78 (0.48), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 310 TYR 0.018 0.002 TYR A 323 PHE 0.015 0.001 PHE A 264 TRP 0.028 0.002 TRP B 128 HIS 0.004 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9718) covalent geometry : angle 0.61703 (13927) hydrogen bonds : bond 0.05091 ( 414) hydrogen bonds : angle 4.63780 ( 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 72 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.9118 (p0) cc_final: 0.7959 (t70) REVERT: A 242 HIS cc_start: 0.8774 (t-170) cc_final: 0.8450 (t70) REVERT: A 243 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.7762 (mmt) REVERT: A 294 TYR cc_start: 0.9462 (m-80) cc_final: 0.9230 (m-80) REVERT: B 74 HIS cc_start: 0.8002 (m-70) cc_final: 0.7782 (m170) REVERT: B 96 LYS cc_start: 0.9471 (mttm) cc_final: 0.9038 (mmmm) REVERT: B 110 MET cc_start: 0.8815 (ptp) cc_final: 0.8486 (ptt) REVERT: B 162 ASP cc_start: 0.9742 (t0) cc_final: 0.9476 (t0) REVERT: B 254 MET cc_start: 0.3273 (ptt) cc_final: 0.3027 (ptt) outliers start: 16 outliers final: 10 residues processed: 68 average time/residue: 0.0680 time to fit residues: 7.1659 Evaluate side-chains 64 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 197 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 243 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 219 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 50 optimal weight: 0.0570 chunk 47 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3505 r_free = 0.3505 target = 0.054879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.038009 restraints weight = 70390.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.039106 restraints weight = 43143.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.039813 restraints weight = 31706.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.040322 restraints weight = 26090.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.040598 restraints weight = 22952.099| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9718 Z= 0.114 Angle : 0.605 9.215 13927 Z= 0.287 Chirality : 0.034 0.208 1672 Planarity : 0.003 0.038 1153 Dihedral : 23.104 177.437 3356 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.60 % Allowed : 17.53 % Favored : 79.87 % 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 aren not related in a simple way. whole: 1.06 (0.34), residues: 692 helix: 1.34 (0.26), residues: 404 sheet: -1.98 (0.63), residues: 72 loop : 0.74 (0.48), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 371 TYR 0.016 0.002 TYR A 323 PHE 0.011 0.001 PHE A 264 TRP 0.027 0.002 TRP B 128 HIS 0.003 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 9718) covalent geometry : angle 0.60546 (13927) hydrogen bonds : bond 0.04703 ( 414) hydrogen bonds : angle 4.50101 ( 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 78 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.274 Fit side-chains REVERT: A 50 GLU cc_start: 0.9405 (mt-10) cc_final: 0.9134 (pt0) REVERT: A 65 ASP cc_start: 0.9074 (p0) cc_final: 0.7895 (t0) REVERT: A 157 TRP cc_start: 0.9457 (m100) cc_final: 0.9145 (m100) REVERT: A 242 HIS cc_start: 0.8737 (t-170) cc_final: 0.8422 (t70) REVERT: A 243 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7713 (mmt) REVERT: A 294 TYR cc_start: 0.9422 (m-80) cc_final: 0.9220 (m-80) REVERT: B 74 HIS cc_start: 0.7977 (m-70) cc_final: 0.7723 (m170) REVERT: B 96 LYS cc_start: 0.9423 (mttm) cc_final: 0.8886 (mmtp) REVERT: B 110 MET cc_start: 0.8732 (ptp) cc_final: 0.8465 (ptt) REVERT: B 162 ASP cc_start: 0.9728 (t0) cc_final: 0.9431 (t0) REVERT: B 179 MET cc_start: 0.8030 (mtm) cc_final: 0.7738 (mtm) REVERT: B 254 MET cc_start: 0.3269 (ptt) cc_final: 0.3007 (ptt) outliers start: 16 outliers final: 10 residues processed: 73 average time/residue: 0.0619 time to fit residues: 7.1116 Evaluate side-chains 68 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 243 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 161 LEU Chi-restraints excluded: chain B residue 187 LEU 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: 10.0000 chunk 13 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3486 r_free = 0.3486 target = 0.054138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.037565 restraints weight = 70249.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.038647 restraints weight = 43233.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.039319 restraints weight = 31732.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.039801 restraints weight = 26167.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.040074 restraints weight = 23023.908| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3590 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= 0.130 Angle : 0.614 14.468 13927 Z= 0.293 Chirality : 0.035 0.205 1672 Planarity : 0.004 0.039 1153 Dihedral : 23.073 177.869 3356 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.27 % Allowed : 18.99 % 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 aren not related in a simple way. whole: 1.02 (0.34), residues: 692 helix: 1.30 (0.26), residues: 404 sheet: -2.03 (0.62), residues: 72 loop : 0.75 (0.48), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 310 TYR 0.020 0.002 TYR A 323 PHE 0.012 0.001 PHE A 264 TRP 0.031 0.002 TRP B 128 HIS 0.003 0.000 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9718) covalent geometry : angle 0.61391 (13927) hydrogen bonds : bond 0.04783 ( 414) hydrogen bonds : angle 4.58171 ( 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 75 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.241 Fit side-chains REVERT: A 50 GLU cc_start: 0.9421 (mt-10) cc_final: 0.9166 (pt0) REVERT: A 65 ASP cc_start: 0.9131 (p0) cc_final: 0.7940 (t0) REVERT: A 133 MET cc_start: 0.9090 (tpt) cc_final: 0.8805 (tpt) REVERT: A 157 TRP cc_start: 0.9423 (m100) cc_final: 0.9129 (m100) REVERT: A 242 HIS cc_start: 0.8749 (t-170) cc_final: 0.8460 (t70) REVERT: B 74 HIS cc_start: 0.8023 (m-70) cc_final: 0.7713 (m170) REVERT: B 96 LYS cc_start: 0.9397 (mttm) cc_final: 0.8879 (mmtp) REVERT: B 110 MET cc_start: 0.8788 (ptp) cc_final: 0.8540 (ptt) REVERT: B 162 ASP cc_start: 0.9749 (t0) cc_final: 0.9458 (t0) REVERT: B 254 MET cc_start: 0.3408 (ptt) cc_final: 0.3128 (ptt) outliers start: 14 outliers final: 12 residues processed: 69 average time/residue: 0.0669 time to fit residues: 7.2566 Evaluate side-chains 67 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU 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 124 LEU 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 123 TYR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 178 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 73 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3443 r_free = 0.3443 target = 0.052258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.035988 restraints weight = 72389.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.037019 restraints weight = 44593.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.037642 restraints weight = 32840.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.038121 restraints weight = 27328.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.038405 restraints weight = 24239.396| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9718 Z= 0.189 Angle : 0.643 14.255 13927 Z= 0.315 Chirality : 0.036 0.202 1672 Planarity : 0.004 0.038 1153 Dihedral : 23.282 176.523 3356 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 24.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.08 % Allowed : 18.99 % Favored : 77.92 % 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 aren not related in a simple way. whole: 0.78 (0.33), residues: 692 helix: 1.09 (0.26), residues: 404 sheet: -2.21 (0.60), residues: 72 loop : 0.73 (0.48), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 310 TYR 0.023 0.002 TYR A 323 PHE 0.023 0.002 PHE A 193 TRP 0.038 0.002 TRP B 128 HIS 0.002 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 9718) covalent geometry : angle 0.64252 (13927) hydrogen bonds : bond 0.05447 ( 414) hydrogen bonds : angle 4.76022 ( 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 75 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9410 (mt-10) cc_final: 0.9148 (pt0) REVERT: A 65 ASP cc_start: 0.9119 (p0) cc_final: 0.8019 (t0) REVERT: A 133 MET cc_start: 0.9123 (tpt) cc_final: 0.8838 (tpt) REVERT: A 242 HIS cc_start: 0.8752 (t-170) cc_final: 0.8441 (t70) REVERT: A 243 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7882 (mmt) REVERT: B 96 LYS cc_start: 0.9439 (mttm) cc_final: 0.8937 (mmtp) REVERT: B 162 ASP cc_start: 0.9757 (t0) cc_final: 0.9496 (t0) REVERT: B 254 MET cc_start: 0.3572 (ptt) cc_final: 0.3293 (ptt) outliers start: 19 outliers final: 16 residues processed: 69 average time/residue: 0.0680 time to fit residues: 7.2109 Evaluate side-chains 71 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU 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 124 LEU 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 243 MET Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 114 LEU 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 219 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 74 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 45 optimal weight: 0.3980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3464 r_free = 0.3464 target = 0.053176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.036535 restraints weight = 72659.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.037611 restraints weight = 44848.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.038287 restraints weight = 33078.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.038760 restraints weight = 27352.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.039089 restraints weight = 24262.738| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3960 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= 0.145 Angle : 0.640 14.570 13927 Z= 0.309 Chirality : 0.035 0.212 1672 Planarity : 0.004 0.038 1153 Dihedral : 23.266 176.274 3356 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.44 % Allowed : 19.97 % Favored : 77.60 % 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 aren not related in a simple way. whole: 0.78 (0.34), residues: 692 helix: 1.19 (0.26), residues: 396 sheet: -2.23 (0.60), residues: 72 loop : 0.54 (0.47), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 310 TYR 0.023 0.002 TYR A 323 PHE 0.045 0.003 PHE A 193 TRP 0.040 0.002 TRP B 128 HIS 0.002 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9718) covalent geometry : angle 0.64003 (13927) hydrogen bonds : bond 0.04974 ( 414) hydrogen bonds : angle 4.66468 ( 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: 15 poor density : 57 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9394 (mt-10) cc_final: 0.9145 (pt0) REVERT: A 133 MET cc_start: 0.9015 (tpt) cc_final: 0.8729 (tpt) REVERT: A 242 HIS cc_start: 0.8709 (t-170) cc_final: 0.8410 (t70) REVERT: B 96 LYS cc_start: 0.9436 (mttm) cc_final: 0.8956 (mmtp) REVERT: B 110 MET cc_start: 0.8894 (ptp) cc_final: 0.8615 (ptt) REVERT: B 162 ASP cc_start: 0.9746 (t0) cc_final: 0.9472 (t0) REVERT: B 254 MET cc_start: 0.3735 (ptt) cc_final: 0.3333 (ptt) outliers start: 15 outliers final: 13 residues processed: 66 average time/residue: 0.0671 time to fit residues: 6.8399 Evaluate side-chains 68 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU 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 197 MET Chi-restraints excluded: chain A residue 322 SER 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 161 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 239 LEU 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: 3.9990 chunk 71 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 78 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3470 r_free = 0.3470 target = 0.053388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.036542 restraints weight = 72097.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.037607 restraints weight = 45028.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.038244 restraints weight = 33263.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.038723 restraints weight = 27801.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.039022 restraints weight = 24624.790| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9718 Z= 0.140 Angle : 0.642 14.411 13927 Z= 0.307 Chirality : 0.035 0.206 1672 Planarity : 0.004 0.039 1153 Dihedral : 23.200 176.979 3356 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.27 % Allowed : 20.29 % Favored : 77.44 % 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 aren not related in a simple way. whole: 0.78 (0.34), residues: 692 helix: 1.20 (0.26), residues: 396 sheet: -2.23 (0.61), residues: 72 loop : 0.52 (0.48), residues: 224 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 0.045 0.002 PHE A 193 TRP 0.040 0.002 TRP B 128 HIS 0.002 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9718) covalent geometry : angle 0.64174 (13927) hydrogen bonds : bond 0.05005 ( 414) hydrogen bonds : angle 4.63483 ( 1057) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1775.76 seconds wall clock time: 31 minutes 30.20 seconds (1890.20 seconds total)