Starting phenix.real_space_refine on Sat Aug 23 08:56:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tlu_41373/08_2025/8tlu_41373.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tlu_41373/08_2025/8tlu_41373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tlu_41373/08_2025/8tlu_41373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tlu_41373/08_2025/8tlu_41373.map" model { file = "/net/cci-nas-00/data/ceres_data/8tlu_41373/08_2025/8tlu_41373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tlu_41373/08_2025/8tlu_41373.cif" } resolution = 3.8 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= 1.000 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 S 30 5.16 5 C 3689 2.51 5 N 885 2.21 5 O 873 1.98 5 H 5703 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11180 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 5606 Classifications: {'peptide': 350} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 335} Chain breaks: 2 Chain: "E" Number of atoms: 5574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5574 Classifications: {'peptide': 348} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 333} Chain breaks: 2 Time building chain proxies: 1.79, per 1000 atoms: 0.16 Number of scatterers: 11180 At special positions: 0 Unit cell: (79.872, 93.184, 74.88, 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 30 16.00 O 873 8.00 N 885 7.00 C 3689 6.00 H 5703 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 215.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1260 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 78.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 Processing helix chain 'A' and resid 15 through 20 removed outlier: 4.007A pdb=" N VAL A 18 " --> pdb=" O GLY A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 53 Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 76 through 91 Processing helix chain 'A' and resid 95 through 121 removed outlier: 4.044A pdb=" N TRP A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 152 Processing helix chain 'A' and resid 174 through 194 removed outlier: 3.761A pdb=" N LEU A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 221 removed outlier: 4.067A pdb=" N ASN A 221 " --> pdb=" O TRP A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 238 through 256 removed outlier: 3.663A pdb=" N VAL A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE A 256 " --> pdb=" O GLY A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 285 removed outlier: 6.029A pdb=" N ALA A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 294 through 314 Processing helix chain 'A' and resid 323 through 332 Processing helix chain 'A' and resid 334 through 359 removed outlier: 3.747A pdb=" N ILE A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 13 through 20 removed outlier: 3.513A pdb=" N PHE E 16 " --> pdb=" O TYR E 13 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL E 18 " --> pdb=" O GLY E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 40 Processing helix chain 'E' and resid 41 through 54 Processing helix chain 'E' and resid 75 through 91 removed outlier: 3.965A pdb=" N ILE E 79 " --> pdb=" O GLY E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 121 removed outlier: 3.672A pdb=" N TRP E 99 " --> pdb=" O ASN E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 152 Processing helix chain 'E' and resid 155 through 159 removed outlier: 3.696A pdb=" N GLN E 159 " --> pdb=" O PRO E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 195 removed outlier: 3.964A pdb=" N ILE E 177 " --> pdb=" O GLY E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 221 removed outlier: 3.775A pdb=" N ASN E 221 " --> pdb=" O TRP E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 229 Processing helix chain 'E' and resid 235 through 237 No H-bonds generated for 'chain 'E' and resid 235 through 237' Processing helix chain 'E' and resid 238 through 255 removed outlier: 3.930A pdb=" N VAL E 242 " --> pdb=" O GLU E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 284 removed outlier: 4.130A pdb=" N GLY E 269 " --> pdb=" O MET E 265 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA E 272 " --> pdb=" O VAL E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 294 Processing helix chain 'E' and resid 294 through 314 Processing helix chain 'E' and resid 323 through 332 Processing helix chain 'E' and resid 334 through 360 removed outlier: 3.562A pdb=" N LEU E 357 " --> pdb=" O GLY E 353 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS E 358 " --> pdb=" O LEU E 354 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG E 360 " --> pdb=" O THR E 356 " (cutoff:3.500A) 395 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.15 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5699 1.03 - 1.23: 4 1.23 - 1.42: 2378 1.42 - 1.61: 3199 1.61 - 1.81: 56 Bond restraints: 11336 Sorted by residual: bond pdb=" CG LEU E 283 " pdb=" CD1 LEU E 283 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.65e+00 bond pdb=" CB THR A 244 " pdb=" CG2 THR A 244 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.67e-01 bond pdb=" CB THR E 244 " pdb=" CG2 THR E 244 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.03e-01 bond pdb=" CB ASP E 195 " pdb=" CG ASP E 195 " ideal model delta sigma weight residual 1.516 1.495 0.021 2.50e-02 1.60e+03 7.18e-01 bond pdb=" CB MET A 348 " pdb=" CG MET A 348 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 7.08e-01 ... (remaining 11331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 20171 1.54 - 3.09: 341 3.09 - 4.63: 31 4.63 - 6.17: 3 6.17 - 7.72: 2 Bond angle restraints: 20548 Sorted by residual: angle pdb=" CB MET E 222 " pdb=" CG MET E 222 " pdb=" SD MET E 222 " ideal model delta sigma weight residual 112.70 120.42 -7.72 3.00e+00 1.11e-01 6.62e+00 angle pdb=" CA LEU E 34 " pdb=" CB LEU E 34 " pdb=" CG LEU E 34 " ideal model delta sigma weight residual 116.30 108.73 7.57 3.50e+00 8.16e-02 4.68e+00 angle pdb=" C ALA A 130 " pdb=" N ARG A 131 " pdb=" CA ARG A 131 " ideal model delta sigma weight residual 121.54 125.03 -3.49 1.91e+00 2.74e-01 3.33e+00 angle pdb=" C TYR A 328 " pdb=" N GLU A 329 " pdb=" CA GLU A 329 " ideal model delta sigma weight residual 120.29 117.70 2.59 1.42e+00 4.96e-01 3.33e+00 angle pdb=" N MET A 203 " pdb=" CA MET A 203 " pdb=" C MET A 203 " ideal model delta sigma weight residual 113.16 110.59 2.57 1.42e+00 4.96e-01 3.27e+00 ... (remaining 20543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.96: 4397 11.96 - 23.92: 549 23.92 - 35.88: 184 35.88 - 47.84: 70 47.84 - 59.79: 85 Dihedral angle restraints: 5285 sinusoidal: 2775 harmonic: 2510 Sorted by residual: dihedral pdb=" CA TYR A 21 " pdb=" C TYR A 21 " pdb=" N LEU A 22 " pdb=" CA LEU A 22 " ideal model delta harmonic sigma weight residual -180.00 -160.04 -19.96 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA HIS A 8 " pdb=" C HIS A 8 " pdb=" N LEU A 9 " pdb=" CA LEU A 9 " ideal model delta harmonic sigma weight residual 180.00 163.05 16.95 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA TYR E 259 " pdb=" C TYR E 259 " pdb=" N PRO E 260 " pdb=" CA PRO E 260 " ideal model delta harmonic sigma weight residual 180.00 164.38 15.62 0 5.00e+00 4.00e-02 9.76e+00 ... (remaining 5282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 568 0.029 - 0.058: 212 0.058 - 0.087: 85 0.087 - 0.116: 25 0.116 - 0.145: 4 Chirality restraints: 894 Sorted by residual: chirality pdb=" CA ILE E 230 " pdb=" N ILE E 230 " pdb=" C ILE E 230 " pdb=" CB ILE E 230 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA PRO E 156 " pdb=" N PRO E 156 " pdb=" C PRO E 156 " pdb=" CB PRO E 156 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE A 230 " pdb=" N ILE A 230 " pdb=" C ILE A 230 " pdb=" CB ILE A 230 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 891 not shown) Planarity restraints: 1585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 259 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO A 260 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 260 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 260 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 131 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C ARG A 131 " -0.029 2.00e-02 2.50e+03 pdb=" O ARG A 131 " 0.011 2.00e-02 2.50e+03 pdb=" N TRP A 132 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 230 " -0.019 5.00e-02 4.00e+02 2.95e-02 1.40e+00 pdb=" N PRO A 231 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 231 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 231 " -0.016 5.00e-02 4.00e+02 ... (remaining 1582 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 760 2.21 - 2.81: 23701 2.81 - 3.40: 32167 3.40 - 4.00: 40703 4.00 - 4.60: 63626 Nonbonded interactions: 160957 Sorted by model distance: nonbonded pdb=" HG SER E 303 " pdb=" O ALA E 322 " model vdw 1.610 2.450 nonbonded pdb=" H3 MET E 1 " pdb=" O LEU E 88 " model vdw 1.638 2.450 nonbonded pdb=" OD1 ASP A 124 " pdb=" H THR A 125 " model vdw 1.645 2.450 nonbonded pdb="HH21 ARG A 337 " pdb=" O PRO E 260 " model vdw 1.671 2.450 nonbonded pdb=" O ALA E 190 " pdb=" HG1 THR E 194 " model vdw 1.680 2.450 ... (remaining 160952 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' and (resid 1 through 121 or resid 129 through 360)) selection = (chain 'E' and (resid 1 through 56 or resid 64 through 360)) } 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: 0.830 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: 0.040 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.590 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 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 : 0.003 0.042 5633 Z= 0.145 Angle : 0.536 7.718 7674 Z= 0.287 Chirality : 0.037 0.145 894 Planarity : 0.004 0.057 921 Dihedral : 12.886 58.139 1926 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: 1.57 (0.32), residues: 686 helix: 1.52 (0.23), residues: 519 sheet: None (None), residues: 0 loop : -0.36 (0.49), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 25 TYR 0.016 0.001 TYR A 21 PHE 0.017 0.001 PHE A 164 TRP 0.008 0.001 TRP E 132 HIS 0.009 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 5633) covalent geometry : angle 0.53558 ( 7674) hydrogen bonds : bond 0.09834 ( 395) hydrogen bonds : angle 5.03233 ( 1167) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8558 (mt) cc_final: 0.8200 (mt) REVERT: A 203 MET cc_start: 0.7984 (tpt) cc_final: 0.6915 (tpt) REVERT: A 232 TYR cc_start: 0.7995 (t80) cc_final: 0.7615 (t80) REVERT: E 203 MET cc_start: 0.7476 (tpt) cc_final: 0.7066 (tpt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1306 time to fit residues: 24.0699 Evaluate side-chains 124 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.166371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.143771 restraints weight = 17951.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.147107 restraints weight = 12460.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.150002 restraints weight = 9567.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.151593 restraints weight = 7957.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.153025 restraints weight = 6914.795| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5633 Z= 0.154 Angle : 0.519 6.522 7674 Z= 0.277 Chirality : 0.037 0.142 894 Planarity : 0.004 0.047 921 Dihedral : 3.791 16.436 752 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.87 % Allowed : 4.90 % Favored : 94.23 % 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: 1.46 (0.32), residues: 686 helix: 1.45 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -0.42 (0.49), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 285 TYR 0.011 0.001 TYR A 176 PHE 0.011 0.001 PHE A 164 TRP 0.006 0.001 TRP A 333 HIS 0.006 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 5633) covalent geometry : angle 0.51938 ( 7674) hydrogen bonds : bond 0.04104 ( 395) hydrogen bonds : angle 4.41484 ( 1167) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 124 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 VAL cc_start: 0.9315 (t) cc_final: 0.9088 (p) REVERT: A 203 MET cc_start: 0.8197 (tpt) cc_final: 0.7838 (mmm) REVERT: A 232 TYR cc_start: 0.8000 (t80) cc_final: 0.7536 (t80) REVERT: E 203 MET cc_start: 0.7697 (tpt) cc_final: 0.7364 (tpt) outliers start: 5 outliers final: 4 residues processed: 125 average time/residue: 0.1573 time to fit residues: 26.5077 Evaluate side-chains 123 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 304 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 2 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.166213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.144680 restraints weight = 17849.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.145261 restraints weight = 14096.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.145668 restraints weight = 12715.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.146160 restraints weight = 11782.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.146417 restraints weight = 10736.216| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5633 Z= 0.139 Angle : 0.498 5.008 7674 Z= 0.264 Chirality : 0.036 0.148 894 Planarity : 0.004 0.043 921 Dihedral : 3.725 16.342 752 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.57 % Allowed : 6.47 % Favored : 91.96 % 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: 1.47 (0.32), residues: 686 helix: 1.46 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -0.47 (0.50), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 285 TYR 0.009 0.001 TYR A 259 PHE 0.009 0.001 PHE A 253 TRP 0.005 0.001 TRP A 99 HIS 0.005 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 5633) covalent geometry : angle 0.49822 ( 7674) hydrogen bonds : bond 0.03921 ( 395) hydrogen bonds : angle 4.28214 ( 1167) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 VAL cc_start: 0.9317 (t) cc_final: 0.9100 (p) REVERT: A 203 MET cc_start: 0.8198 (tpt) cc_final: 0.7365 (tpt) REVERT: E 222 MET cc_start: 0.6173 (mmp) cc_final: 0.5857 (mmp) outliers start: 9 outliers final: 8 residues processed: 122 average time/residue: 0.1570 time to fit residues: 25.6903 Evaluate side-chains 122 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 311 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 57 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 0.0000 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.168088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.145527 restraints weight = 17707.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.149024 restraints weight = 12265.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.151813 restraints weight = 9391.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.153887 restraints weight = 7589.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.154975 restraints weight = 6615.094| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5633 Z= 0.108 Angle : 0.470 4.732 7674 Z= 0.246 Chirality : 0.036 0.143 894 Planarity : 0.004 0.046 921 Dihedral : 3.621 16.232 752 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.40 % Allowed : 7.69 % Favored : 90.91 % 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: 1.74 (0.32), residues: 686 helix: 1.67 (0.22), residues: 519 sheet: None (None), residues: 0 loop : -0.37 (0.50), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 360 TYR 0.009 0.001 TYR A 176 PHE 0.007 0.001 PHE A 253 TRP 0.004 0.000 TRP A 99 HIS 0.004 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 5633) covalent geometry : angle 0.47022 ( 7674) hydrogen bonds : bond 0.03675 ( 395) hydrogen bonds : angle 4.11492 ( 1167) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 VAL cc_start: 0.9290 (t) cc_final: 0.9083 (p) REVERT: A 181 TYR cc_start: 0.8496 (t80) cc_final: 0.8240 (t80) REVERT: A 203 MET cc_start: 0.8227 (tpt) cc_final: 0.7452 (tpt) REVERT: E 203 MET cc_start: 0.7639 (tpt) cc_final: 0.7194 (tpt) REVERT: E 222 MET cc_start: 0.6205 (mmp) cc_final: 0.5994 (mmp) REVERT: E 271 LEU cc_start: 0.9001 (mt) cc_final: 0.8741 (mp) outliers start: 8 outliers final: 7 residues processed: 127 average time/residue: 0.1286 time to fit residues: 22.7268 Evaluate side-chains 130 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 311 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.167423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.145280 restraints weight = 17660.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.148434 restraints weight = 12217.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.151163 restraints weight = 9497.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.152783 restraints weight = 7867.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.154322 restraints weight = 6802.756| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5633 Z= 0.116 Angle : 0.472 4.706 7674 Z= 0.248 Chirality : 0.036 0.143 894 Planarity : 0.004 0.047 921 Dihedral : 3.576 16.281 752 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.40 % Allowed : 8.57 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.32), residues: 686 helix: 1.74 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -0.36 (0.50), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 360 TYR 0.007 0.001 TYR A 176 PHE 0.011 0.001 PHE A 66 TRP 0.004 0.001 TRP A 99 HIS 0.004 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 5633) covalent geometry : angle 0.47204 ( 7674) hydrogen bonds : bond 0.03662 ( 395) hydrogen bonds : angle 4.07262 ( 1167) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 VAL cc_start: 0.9295 (t) cc_final: 0.9046 (p) REVERT: A 117 TYR cc_start: 0.6409 (t80) cc_final: 0.6155 (t80) REVERT: A 181 TYR cc_start: 0.8535 (t80) cc_final: 0.8247 (t80) REVERT: A 195 ASP cc_start: 0.8215 (t70) cc_final: 0.8006 (t70) REVERT: A 203 MET cc_start: 0.8204 (tpt) cc_final: 0.7449 (tpt) REVERT: A 219 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.8024 (m) REVERT: A 259 TYR cc_start: 0.8059 (t80) cc_final: 0.7819 (t80) REVERT: A 307 GLN cc_start: 0.8944 (tt0) cc_final: 0.8631 (tt0) REVERT: E 222 MET cc_start: 0.6289 (mmp) cc_final: 0.6060 (mmp) outliers start: 8 outliers final: 7 residues processed: 129 average time/residue: 0.1347 time to fit residues: 24.0602 Evaluate side-chains 132 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 311 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 57 optimal weight: 0.1980 chunk 66 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.166780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.144393 restraints weight = 17889.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.147850 restraints weight = 12431.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.150605 restraints weight = 9505.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.152586 restraints weight = 7699.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.153603 restraints weight = 6721.978| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5633 Z= 0.118 Angle : 0.471 4.930 7674 Z= 0.248 Chirality : 0.036 0.142 894 Planarity : 0.004 0.047 921 Dihedral : 3.553 16.357 752 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.75 % Allowed : 9.27 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.32), residues: 686 helix: 1.80 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -0.30 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 285 TYR 0.010 0.001 TYR E 97 PHE 0.006 0.001 PHE A 66 TRP 0.004 0.001 TRP A 99 HIS 0.004 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 5633) covalent geometry : angle 0.47150 ( 7674) hydrogen bonds : bond 0.03646 ( 395) hydrogen bonds : angle 4.06491 ( 1167) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.3849 (OUTLIER) cc_final: 0.2296 (p90) REVERT: A 106 VAL cc_start: 0.9299 (t) cc_final: 0.9090 (p) REVERT: A 181 TYR cc_start: 0.8519 (t80) cc_final: 0.8196 (t80) REVERT: A 195 ASP cc_start: 0.8308 (t70) cc_final: 0.8082 (t70) REVERT: A 203 MET cc_start: 0.8198 (tpt) cc_final: 0.7465 (tpt) REVERT: A 219 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.8029 (m) REVERT: E 222 MET cc_start: 0.6403 (mmp) cc_final: 0.6167 (mmp) outliers start: 10 outliers final: 7 residues processed: 130 average time/residue: 0.1130 time to fit residues: 20.8942 Evaluate side-chains 133 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 311 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.167444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.145111 restraints weight = 17648.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.148432 restraints weight = 12266.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.151070 restraints weight = 9532.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.152978 restraints weight = 7799.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.154042 restraints weight = 6707.858| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5633 Z= 0.112 Angle : 0.468 4.701 7674 Z= 0.245 Chirality : 0.036 0.140 894 Planarity : 0.004 0.048 921 Dihedral : 3.534 16.533 752 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.57 % Allowed : 9.44 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.32), residues: 686 helix: 1.86 (0.22), residues: 519 sheet: None (None), residues: 0 loop : -0.29 (0.51), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 285 TYR 0.010 0.001 TYR E 97 PHE 0.007 0.001 PHE A 66 TRP 0.004 0.001 TRP A 99 HIS 0.004 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 5633) covalent geometry : angle 0.46813 ( 7674) hydrogen bonds : bond 0.03596 ( 395) hydrogen bonds : angle 4.01349 ( 1167) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.3855 (OUTLIER) cc_final: 0.2306 (p90) REVERT: A 106 VAL cc_start: 0.9281 (t) cc_final: 0.9047 (p) REVERT: A 181 TYR cc_start: 0.8527 (t80) cc_final: 0.8192 (t80) REVERT: A 195 ASP cc_start: 0.8302 (t70) cc_final: 0.8080 (t70) REVERT: A 203 MET cc_start: 0.8193 (tpt) cc_final: 0.7491 (tpt) REVERT: A 219 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7985 (m) REVERT: E 222 MET cc_start: 0.6549 (mmp) cc_final: 0.6297 (mmp) outliers start: 9 outliers final: 6 residues processed: 129 average time/residue: 0.1249 time to fit residues: 22.5589 Evaluate side-chains 129 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 311 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.165139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.142534 restraints weight = 17929.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.145471 restraints weight = 12549.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.148365 restraints weight = 9884.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.149955 restraints weight = 8238.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.151329 restraints weight = 7177.394| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5633 Z= 0.138 Angle : 0.487 4.767 7674 Z= 0.259 Chirality : 0.036 0.156 894 Planarity : 0.004 0.050 921 Dihedral : 3.586 16.809 752 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.75 % Allowed : 10.49 % Favored : 87.76 % 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 aren not related in a simple way. whole: 1.84 (0.32), residues: 686 helix: 1.73 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -0.35 (0.51), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 285 TYR 0.009 0.001 TYR E 97 PHE 0.008 0.001 PHE E 253 TRP 0.005 0.001 TRP A 99 HIS 0.004 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 5633) covalent geometry : angle 0.48746 ( 7674) hydrogen bonds : bond 0.03730 ( 395) hydrogen bonds : angle 4.09465 ( 1167) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.3871 (OUTLIER) cc_final: 0.2269 (p90) REVERT: A 106 VAL cc_start: 0.9315 (t) cc_final: 0.9094 (p) REVERT: A 181 TYR cc_start: 0.8536 (t80) cc_final: 0.8194 (t80) REVERT: A 195 ASP cc_start: 0.8376 (t70) cc_final: 0.8052 (t70) REVERT: A 203 MET cc_start: 0.8199 (tpt) cc_final: 0.7483 (tpt) REVERT: E 222 MET cc_start: 0.6788 (mmp) cc_final: 0.6347 (mmp) outliers start: 10 outliers final: 8 residues processed: 128 average time/residue: 0.1251 time to fit residues: 22.1620 Evaluate side-chains 131 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 311 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.166057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.143689 restraints weight = 17849.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.147010 restraints weight = 12469.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.149730 restraints weight = 9633.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.150862 restraints weight = 7823.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.150913 restraints weight = 7040.811| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5633 Z= 0.120 Angle : 0.487 4.766 7674 Z= 0.254 Chirality : 0.036 0.141 894 Planarity : 0.004 0.050 921 Dihedral : 3.569 16.569 752 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.57 % Allowed : 10.66 % Favored : 87.76 % 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 aren not related in a simple way. whole: 1.92 (0.32), residues: 686 helix: 1.81 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -0.37 (0.51), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 285 TYR 0.008 0.001 TYR E 97 PHE 0.007 0.001 PHE A 66 TRP 0.005 0.001 TRP A 99 HIS 0.004 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 5633) covalent geometry : angle 0.48745 ( 7674) hydrogen bonds : bond 0.03689 ( 395) hydrogen bonds : angle 4.06387 ( 1167) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.3943 (OUTLIER) cc_final: 0.2365 (p90) REVERT: A 106 VAL cc_start: 0.9310 (t) cc_final: 0.9089 (p) REVERT: A 181 TYR cc_start: 0.8537 (t80) cc_final: 0.8191 (t80) REVERT: A 195 ASP cc_start: 0.8336 (t70) cc_final: 0.8004 (t70) REVERT: A 203 MET cc_start: 0.8209 (tpt) cc_final: 0.7496 (tpt) REVERT: E 222 MET cc_start: 0.6724 (mmp) cc_final: 0.6366 (mmp) outliers start: 9 outliers final: 8 residues processed: 125 average time/residue: 0.1308 time to fit residues: 22.6075 Evaluate side-chains 130 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 311 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.166279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.143682 restraints weight = 17733.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.147120 restraints weight = 12428.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.149361 restraints weight = 9667.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.151608 restraints weight = 8053.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.152678 restraints weight = 6902.974| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5633 Z= 0.119 Angle : 0.483 4.755 7674 Z= 0.252 Chirality : 0.036 0.139 894 Planarity : 0.004 0.051 921 Dihedral : 3.558 16.037 752 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.57 % Allowed : 10.84 % Favored : 87.59 % 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: 1.96 (0.32), residues: 686 helix: 1.83 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -0.35 (0.51), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 285 TYR 0.008 0.001 TYR E 97 PHE 0.006 0.001 PHE A 66 TRP 0.004 0.001 TRP A 99 HIS 0.003 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 5633) covalent geometry : angle 0.48295 ( 7674) hydrogen bonds : bond 0.03661 ( 395) hydrogen bonds : angle 4.04843 ( 1167) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.3909 (OUTLIER) cc_final: 0.2348 (p90) REVERT: A 106 VAL cc_start: 0.9305 (t) cc_final: 0.9087 (p) REVERT: A 181 TYR cc_start: 0.8523 (t80) cc_final: 0.8136 (t80) REVERT: A 195 ASP cc_start: 0.8339 (t70) cc_final: 0.7999 (t70) REVERT: A 203 MET cc_start: 0.8199 (tpt) cc_final: 0.7469 (tpt) REVERT: E 222 MET cc_start: 0.6793 (mmp) cc_final: 0.6444 (mmp) outliers start: 9 outliers final: 7 residues processed: 127 average time/residue: 0.1250 time to fit residues: 22.2441 Evaluate side-chains 132 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain E residue 304 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.0570 chunk 44 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 45 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.167624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.145332 restraints weight = 17789.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.148820 restraints weight = 12393.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.151138 restraints weight = 9576.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.153185 restraints weight = 7958.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.154746 restraints weight = 6775.681| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5633 Z= 0.107 Angle : 0.483 4.683 7674 Z= 0.249 Chirality : 0.036 0.136 894 Planarity : 0.004 0.051 921 Dihedral : 3.523 15.853 752 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.57 % Allowed : 11.36 % Favored : 87.06 % 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: 2.08 (0.32), residues: 686 helix: 1.91 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -0.29 (0.51), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 285 TYR 0.007 0.001 TYR E 97 PHE 0.006 0.001 PHE A 66 TRP 0.005 0.001 TRP A 99 HIS 0.003 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 5633) covalent geometry : angle 0.48261 ( 7674) hydrogen bonds : bond 0.03598 ( 395) hydrogen bonds : angle 3.99831 ( 1167) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1893.58 seconds wall clock time: 32 minutes 50.79 seconds (1970.79 seconds total)