Starting phenix.real_space_refine on Thu Jul 2 05:24:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9teo_55831/07_2026/9teo_55831.cif Found real_map, /net/cci-nas-00/data/ceres_data/9teo_55831/07_2026/9teo_55831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9teo_55831/07_2026/9teo_55831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9teo_55831/07_2026/9teo_55831.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9teo_55831/07_2026/9teo_55831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9teo_55831/07_2026/9teo_55831.map" } resolution = 3.27 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= 0.001 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 54 5.49 5 S 18 5.16 5 C 4029 2.51 5 N 1200 2.21 5 O 1383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6686 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3540 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 28, 'TRANS': 424} Chain: "B" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 326 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "E" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 563 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "F" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 544 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "I" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1711 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1778 SG CYS A 366 61.738 68.147 29.625 1.00107.09 S ATOM 1793 SG CYS A 368 58.395 66.868 28.305 1.00124.57 S ATOM 1938 SG CYS A 387 61.656 66.362 26.216 1.00112.94 S ATOM 5722 SG CYS I 117 89.176 74.980 53.534 1.00 95.97 S ATOM 5860 SG CYS I 135 88.304 78.685 53.018 1.00112.08 S ATOM 5870 SG CYS I 137 85.511 76.183 53.776 1.00102.39 S Time building chain proxies: 1.49, per 1000 atoms: 0.22 Number of scatterers: 6686 At special positions: 0 Unit cell: (120.84, 94.34, 87.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 18 16.00 P 54 15.00 O 1383 8.00 N 1200 7.00 C 4029 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: 0.57 Conformation dependent library (CDL) restraints added in 340.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 401 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 366 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 368 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 387 " pdb=" ZN I 301 " pdb="ZN ZN I 301 " - pdb=" NE2 HIS I 115 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 135 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 117 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 137 " Number of angles added : 6 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1306 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 7 sheets defined 42.1% alpha, 23.2% beta 26 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 140 through 163 Processing helix chain 'A' and resid 211 through 226 Processing helix chain 'A' and resid 243 through 254 Processing helix chain 'A' and resid 258 through 264 Processing helix chain 'A' and resid 273 through 282 Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 331 through 343 Processing helix chain 'A' and resid 379 through 382 Processing helix chain 'A' and resid 409 through 426 Processing helix chain 'A' and resid 430 through 444 Processing helix chain 'A' and resid 453 through 481 removed outlier: 4.224A pdb=" N ARG A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 517 Processing helix chain 'A' and resid 540 through 545 Processing helix chain 'A' and resid 546 through 557 Processing helix chain 'A' and resid 575 through 578 Processing helix chain 'B' and resid 464 through 480 Processing helix chain 'B' and resid 485 through 502 Processing helix chain 'I' and resid 56 through 68 Processing helix chain 'I' and resid 127 through 131 Processing helix chain 'I' and resid 140 through 150 removed outlier: 3.582A pdb=" N GLU I 150 " --> pdb=" O ALA I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 171 removed outlier: 3.972A pdb=" N GLY I 171 " --> pdb=" O PRO I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 198 removed outlier: 3.655A pdb=" N VAL I 185 " --> pdb=" O THR I 181 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N HIS I 187 " --> pdb=" O PHE I 183 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLU I 188 " --> pdb=" O LYS I 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 185 Processing sheet with id=AA2, first strand: chain 'A' and resid 291 through 297 removed outlier: 5.561A pdb=" N LYS A 296 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE A 307 " --> pdb=" O LYS A 296 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 364 through 366 Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 375 Processing sheet with id=AA5, first strand: chain 'I' and resid 27 through 36 removed outlier: 9.428A pdb=" N GLY I 27 " --> pdb=" O ARG I 51 " (cutoff:3.500A) removed outlier: 10.848A pdb=" N ARG I 51 " --> pdb=" O GLY I 27 " (cutoff:3.500A) removed outlier: 9.938A pdb=" N PHE I 29 " --> pdb=" O LYS I 49 " (cutoff:3.500A) removed outlier: 11.490A pdb=" N LYS I 49 " --> pdb=" O PHE I 29 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N SER I 31 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE I 83 " --> pdb=" O THR I 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 122 through 124 removed outlier: 7.763A pdb=" N HIS I 116 " --> pdb=" O VAL I 123 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU I 109 " --> pdb=" O LEU I 113 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N ALA I 98 " --> pdb=" O THR I 163 " (cutoff:3.500A) removed outlier: 12.443A pdb=" N THR I 163 " --> pdb=" O ALA I 98 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLY I 100 " --> pdb=" O THR I 161 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP I 104 " --> pdb=" O ALA I 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 122 through 124 removed outlier: 7.763A pdb=" N HIS I 116 " --> pdb=" O VAL I 123 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU I 109 " --> pdb=" O LEU I 113 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU I 203 " --> pdb=" O LEU I 235 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR I 233 " --> pdb=" O ASN I 205 " (cutoff:3.500A) 284 hydrogen bonds defined for protein. 810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 0.72 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: 1746 1.33 - 1.45: 1501 1.45 - 1.57: 3561 1.57 - 1.69: 106 1.69 - 1.81: 27 Bond restraints: 6941 Sorted by residual: bond pdb=" C3' DT E 53 " pdb=" C2' DT E 53 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DG F 24 " pdb=" C2' DG F 24 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.63e+00 bond pdb=" C3' DA F 21 " pdb=" C2' DA F 21 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.52e+00 bond pdb=" C3' DC E 51 " pdb=" C2' DC E 51 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.19e+00 bond pdb=" C3' DT E 36 " pdb=" C2' DT E 36 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.93e+00 ... (remaining 6936 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 9405 1.86 - 3.73: 203 3.73 - 5.59: 9 5.59 - 7.45: 3 7.45 - 9.31: 1 Bond angle restraints: 9621 Sorted by residual: angle pdb=" N3 DT F 28 " pdb=" C4 DT F 28 " pdb=" O4 DT F 28 " ideal model delta sigma weight residual 119.90 122.71 -2.81 6.00e-01 2.78e+00 2.20e+01 angle pdb=" N3 DT E 40 " pdb=" C4 DT E 40 " pdb=" O4 DT E 40 " ideal model delta sigma weight residual 119.90 122.70 -2.80 6.00e-01 2.78e+00 2.17e+01 angle pdb=" O4' DC F 4 " pdb=" C4' DC F 4 " pdb=" C3' DC F 4 " ideal model delta sigma weight residual 106.00 103.29 2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" O4' DG E 47 " pdb=" C4' DG E 47 " pdb=" C3' DG E 47 " ideal model delta sigma weight residual 106.00 103.34 2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT F 19 " pdb=" C4 DT F 19 " pdb=" O4 DT F 19 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 ... (remaining 9616 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 3148 17.89 - 35.78: 553 35.78 - 53.67: 254 53.67 - 71.56: 68 71.56 - 89.45: 9 Dihedral angle restraints: 4032 sinusoidal: 2001 harmonic: 2031 Sorted by residual: dihedral pdb=" CB GLU A 431 " pdb=" CG GLU A 431 " pdb=" CD GLU A 431 " pdb=" OE1 GLU A 431 " ideal model delta sinusoidal sigma weight residual 0.00 89.45 -89.45 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 183 " pdb=" CG GLU A 183 " pdb=" CD GLU A 183 " pdb=" OE1 GLU A 183 " ideal model delta sinusoidal sigma weight residual 0.00 -86.76 86.76 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU A 439 " pdb=" CG GLU A 439 " pdb=" CD GLU A 439 " pdb=" OE1 GLU A 439 " ideal model delta sinusoidal sigma weight residual 0.00 86.61 -86.61 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 4029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 623 0.028 - 0.057: 252 0.057 - 0.085: 76 0.085 - 0.113: 75 0.113 - 0.141: 14 Chirality restraints: 1040 Sorted by residual: chirality pdb=" C3' DA F 17 " pdb=" C4' DA F 17 " pdb=" O3' DA F 17 " pdb=" C2' DA F 17 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CG LEU B 474 " pdb=" CB LEU B 474 " pdb=" CD1 LEU B 474 " pdb=" CD2 LEU B 474 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE I 95 " pdb=" N ILE I 95 " pdb=" C ILE I 95 " pdb=" CB ILE I 95 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 1037 not shown) Planarity restraints: 1070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 273 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO A 274 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 274 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 274 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 153 " -0.021 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO I 154 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO I 154 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO I 154 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT E 38 " -0.016 2.00e-02 2.50e+03 7.96e-03 1.58e+00 pdb=" N1 DT E 38 " 0.017 2.00e-02 2.50e+03 pdb=" C2 DT E 38 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DT E 38 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DT E 38 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT E 38 " -0.004 2.00e-02 2.50e+03 pdb=" O4 DT E 38 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DT E 38 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT E 38 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DT E 38 " 0.003 2.00e-02 2.50e+03 ... (remaining 1067 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 3273 2.99 - 3.47: 6767 3.47 - 3.94: 11712 3.94 - 4.42: 13270 4.42 - 4.90: 19944 Nonbonded interactions: 54966 Sorted by model distance: nonbonded pdb=" O5' DG E 48 " pdb=" O4' DG E 48 " model vdw 2.512 2.432 nonbonded pdb=" O5' DG E 57 " pdb=" O4' DG E 57 " model vdw 2.567 2.432 nonbonded pdb=" N1 DG E 47 " pdb=" C4 DG E 47 " model vdw 2.595 2.672 nonbonded pdb=" N1 DG E 32 " pdb=" C4 DG E 32 " model vdw 2.596 2.672 nonbonded pdb=" N1 DG E 34 " pdb=" C4 DG E 34 " model vdw 2.596 2.672 ... (remaining 54961 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.300 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.290 Find NCS groups from input model: 0.030 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5313 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 0.042 6949 Z= 0.339 Angle : 0.589 9.315 9627 Z= 0.444 Chirality : 0.042 0.141 1040 Planarity : 0.004 0.037 1070 Dihedral : 21.619 89.446 2726 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.69 % Allowed : 22.34 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.32), residues: 705 helix: 2.28 (0.30), residues: 270 sheet: -1.03 (0.54), residues: 101 loop : 0.01 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 189 TYR 0.008 0.001 TYR A 475 PHE 0.009 0.001 PHE A 444 TRP 0.009 0.001 TRP I 103 HIS 0.004 0.001 HIS I 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.34 ( 6941) covalent geometry : angle 0.58875 / 0.44 ( 9621) hydrogen bonds : bond 0.12448 / 8.93 ( 347) hydrogen bonds : angle 6.49764 / 4.50 ( 946) metal coordination : bond 0.01255 / 0.76 ( 8) metal coordination : angle 1.31306 / 1.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 155 time to evaluate : 0.222 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 195 ILE cc_start: 0.7336 (pt) cc_final: 0.6659 (pt) REVERT: A 460 LEU cc_start: 0.7020 (mt) cc_final: 0.6716 (tp) REVERT: A 468 LEU cc_start: 0.8162 (mt) cc_final: 0.7691 (mp) REVERT: A 489 ARG cc_start: 0.6177 (ppt170) cc_final: 0.5967 (ppt170) REVERT: B 471 LEU cc_start: 0.7941 (mt) cc_final: 0.7556 (mt) REVERT: B 475 TYR cc_start: 0.7526 (m-80) cc_final: 0.7159 (m-80) REVERT: B 476 GLU cc_start: 0.6919 (pt0) cc_final: 0.6574 (pt0) REVERT: B 493 ARG cc_start: 0.8531 (mmt90) cc_final: 0.8269 (mtt90) outliers start: 4 outliers final: 1 residues processed: 157 average time/residue: 0.0866 time to fit residues: 17.3304 Evaluate side-chains 90 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 ASN ** 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 = 0.3721 r_free = 0.3721 target = 0.088632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.071225 restraints weight = 20272.773| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.93 r_work: 0.3228 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 6949 Z= 0.344 Angle : 0.978 13.625 9627 Z= 0.538 Chirality : 0.052 0.251 1040 Planarity : 0.009 0.155 1070 Dihedral : 22.922 78.917 1354 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.33 % Allowed : 21.99 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.31), residues: 705 helix: 0.61 (0.30), residues: 268 sheet: -1.56 (0.48), residues: 113 loop : -0.64 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 28 TYR 0.029 0.005 TYR I 238 PHE 0.021 0.003 PHE A 209 TRP 0.050 0.005 TRP A 584 HIS 0.013 0.003 HIS A 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00729 / 0.34 ( 6941) covalent geometry : angle 0.96964 / 0.54 ( 9621) hydrogen bonds : bond 0.06199 / 4.15 ( 347) hydrogen bonds : angle 5.42150 / 3.82 ( 946) metal coordination : bond 0.03053 / 1.57 ( 8) metal coordination : angle 5.31743 / 4.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 LEU cc_start: 0.8455 (mt) cc_final: 0.8245 (pp) REVERT: B 471 LEU cc_start: 0.7787 (mt) cc_final: 0.7128 (mt) REVERT: B 475 TYR cc_start: 0.7547 (m-80) cc_final: 0.7231 (m-80) REVERT: B 493 ARG cc_start: 0.8376 (mmt90) cc_final: 0.8074 (mtt90) REVERT: I 82 PHE cc_start: 0.7082 (p90) cc_final: 0.6297 (p90) REVERT: I 203 LEU cc_start: 0.7525 (tt) cc_final: 0.6798 (mp) outliers start: 31 outliers final: 6 residues processed: 132 average time/residue: 0.0753 time to fit residues: 13.1510 Evaluate side-chains 92 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 231 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 27 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 503 GLN I 30 HIS I 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.087694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.069652 restraints weight = 19841.080| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.99 r_work: 0.3158 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.6093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6949 Z= 0.190 Angle : 0.673 10.898 9627 Z= 0.378 Chirality : 0.045 0.230 1040 Planarity : 0.005 0.045 1070 Dihedral : 22.435 73.653 1353 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.75 % Allowed : 23.71 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.32), residues: 705 helix: 1.28 (0.30), residues: 273 sheet: -1.63 (0.44), residues: 133 loop : -0.36 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 39 TYR 0.023 0.002 TYR I 151 PHE 0.010 0.002 PHE A 289 TRP 0.029 0.002 TRP A 220 HIS 0.005 0.001 HIS I 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.19 ( 6941) covalent geometry : angle 0.66790 / 0.38 ( 9621) hydrogen bonds : bond 0.04749 / 3.23 ( 347) hydrogen bonds : angle 5.14816 / 3.60 ( 946) metal coordination : bond 0.02306 / 1.16 ( 8) metal coordination : angle 3.49470 / 3.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 203 LEU cc_start: 0.7817 (tt) cc_final: 0.6904 (mp) REVERT: I 210 LEU cc_start: 0.6265 (OUTLIER) cc_final: 0.5995 (tt) outliers start: 16 outliers final: 6 residues processed: 92 average time/residue: 0.0896 time to fit residues: 10.7963 Evaluate side-chains 78 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 151 TYR Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain I residue 238 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 67 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 7 optimal weight: 0.0980 chunk 70 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.088246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.069989 restraints weight = 20138.380| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.01 r_work: 0.3180 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.6795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6949 Z= 0.157 Angle : 0.648 8.535 9627 Z= 0.358 Chirality : 0.043 0.337 1040 Planarity : 0.004 0.038 1070 Dihedral : 22.350 75.168 1353 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.58 % Allowed : 24.40 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.33), residues: 705 helix: 1.51 (0.31), residues: 274 sheet: -1.79 (0.43), residues: 133 loop : -0.32 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 478 TYR 0.011 0.002 TYR A 475 PHE 0.016 0.002 PHE I 183 TRP 0.018 0.002 TRP I 103 HIS 0.003 0.001 HIS A 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.16 ( 6941) covalent geometry : angle 0.64559 / 0.36 ( 9621) hydrogen bonds : bond 0.04182 / 2.89 ( 347) hydrogen bonds : angle 4.79511 / 3.34 ( 946) metal coordination : bond 0.01499 / 0.80 ( 8) metal coordination : angle 2.27687 / 2.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 ASP cc_start: 0.6498 (m-30) cc_final: 0.6061 (t70) REVERT: A 478 ARG cc_start: 0.6553 (OUTLIER) cc_final: 0.6289 (tpt170) REVERT: I 203 LEU cc_start: 0.8139 (tt) cc_final: 0.7014 (mp) REVERT: I 210 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6361 (tt) outliers start: 15 outliers final: 8 residues processed: 88 average time/residue: 0.1004 time to fit residues: 11.3185 Evaluate side-chains 70 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 151 TYR Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain I residue 238 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 7 optimal weight: 0.0980 chunk 4 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 222 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.088548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.069773 restraints weight = 20198.902| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.04 r_work: 0.3168 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.8299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 6949 Z= 0.197 Angle : 0.686 15.366 9627 Z= 0.378 Chirality : 0.044 0.227 1040 Planarity : 0.006 0.074 1070 Dihedral : 22.537 77.695 1353 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.61 % Allowed : 23.88 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.32), residues: 705 helix: 1.41 (0.31), residues: 275 sheet: -1.94 (0.44), residues: 132 loop : -0.37 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 390 TYR 0.013 0.001 TYR I 151 PHE 0.024 0.002 PHE A 557 TRP 0.020 0.002 TRP A 584 HIS 0.010 0.001 HIS I 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 ( 6941) covalent geometry : angle 0.68226 / 0.38 ( 9621) hydrogen bonds : bond 0.04341 / 2.93 ( 347) hydrogen bonds : angle 4.78978 / 3.35 ( 946) metal coordination : bond 0.02960 / 1.66 ( 8) metal coordination : angle 2.84056 / 2.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 ASP cc_start: 0.7098 (m-30) cc_final: 0.6674 (t70) REVERT: A 468 LEU cc_start: 0.9001 (mt) cc_final: 0.8767 (mp) REVERT: I 210 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6598 (tt) outliers start: 21 outliers final: 10 residues processed: 81 average time/residue: 0.0864 time to fit residues: 9.3001 Evaluate side-chains 66 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 135 CYS Chi-restraints excluded: chain I residue 151 TYR Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain I residue 238 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 71 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 GLN I 133 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.088155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.069109 restraints weight = 20107.703| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.03 r_work: 0.3158 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.9483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6949 Z= 0.195 Angle : 0.697 14.339 9627 Z= 0.373 Chirality : 0.045 0.426 1040 Planarity : 0.005 0.039 1070 Dihedral : 22.497 77.025 1353 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.09 % Allowed : 23.88 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.32), residues: 705 helix: 1.43 (0.30), residues: 275 sheet: -2.15 (0.43), residues: 129 loop : -0.31 (0.38), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG A 189 TYR 0.030 0.002 TYR I 228 PHE 0.015 0.002 PHE A 553 TRP 0.020 0.002 TRP I 50 HIS 0.006 0.001 HIS A 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.19 ( 6941) covalent geometry : angle 0.69315 / 0.37 ( 9621) hydrogen bonds : bond 0.04210 / 2.86 ( 347) hydrogen bonds : angle 4.83139 / 3.35 ( 946) metal coordination : bond 0.01956 / 1.00 ( 8) metal coordination : angle 3.10889 / 2.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 ASP cc_start: 0.7673 (m-30) cc_final: 0.7289 (t70) REVERT: A 457 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7886 (ptm-80) REVERT: B 493 ARG cc_start: 0.8665 (mtt90) cc_final: 0.8045 (mpt-90) REVERT: I 161 THR cc_start: 0.8323 (OUTLIER) cc_final: 0.8121 (m) REVERT: I 221 ARG cc_start: 0.5944 (ptp90) cc_final: 0.5665 (ptp90) outliers start: 18 outliers final: 8 residues processed: 82 average time/residue: 0.0997 time to fit residues: 10.6312 Evaluate side-chains 68 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 151 TYR Chi-restraints excluded: chain I residue 161 THR Chi-restraints excluded: chain I residue 211 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 42 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 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 = 0.3679 r_free = 0.3679 target = 0.087525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.068119 restraints weight = 19812.115| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.02 r_work: 0.3117 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 1.0464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6949 Z= 0.204 Angle : 0.679 10.153 9627 Z= 0.375 Chirality : 0.044 0.285 1040 Planarity : 0.005 0.038 1070 Dihedral : 22.490 75.347 1353 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.92 % Allowed : 24.74 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.33), residues: 705 helix: 1.47 (0.31), residues: 274 sheet: -2.15 (0.43), residues: 129 loop : -0.41 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 442 TYR 0.032 0.002 TYR B 475 PHE 0.013 0.002 PHE A 289 TRP 0.045 0.002 TRP A 438 HIS 0.004 0.001 HIS I 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.20 ( 6941) covalent geometry : angle 0.67515 / 0.37 ( 9621) hydrogen bonds : bond 0.04159 / 2.78 ( 347) hydrogen bonds : angle 4.82856 / 3.38 ( 946) metal coordination : bond 0.02390 / 1.34 ( 8) metal coordination : angle 3.14563 / 1.86 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 278 MET cc_start: 0.8611 (tpt) cc_final: 0.8406 (ttt) REVERT: A 343 ASP cc_start: 0.7939 (m-30) cc_final: 0.7494 (m-30) REVERT: A 404 THR cc_start: 0.7262 (m) cc_final: 0.6859 (p) REVERT: A 437 LEU cc_start: 0.8924 (tp) cc_final: 0.8665 (tp) REVERT: A 457 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8018 (ptm-80) REVERT: A 471 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7587 (mt) outliers start: 17 outliers final: 11 residues processed: 72 average time/residue: 0.0976 time to fit residues: 8.8711 Evaluate side-chains 65 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 80 GLU Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 151 TYR Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain I residue 216 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 0.3980 chunk 56 optimal weight: 5.9990 chunk 6 optimal weight: 0.2980 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 16 optimal weight: 0.2980 chunk 40 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.087837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.068500 restraints weight = 19903.530| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.02 r_work: 0.3139 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 1.0717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6949 Z= 0.148 Angle : 0.638 8.313 9627 Z= 0.351 Chirality : 0.042 0.258 1040 Planarity : 0.004 0.038 1070 Dihedral : 22.355 75.518 1353 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.89 % Allowed : 25.09 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.33), residues: 705 helix: 1.69 (0.31), residues: 274 sheet: -2.15 (0.43), residues: 129 loop : -0.28 (0.39), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 189 TYR 0.033 0.002 TYR B 475 PHE 0.016 0.001 PHE A 492 TRP 0.036 0.002 TRP A 438 HIS 0.004 0.001 HIS I 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 ( 6941) covalent geometry : angle 0.63561 / 0.35 ( 9621) hydrogen bonds : bond 0.03909 / 2.64 ( 347) hydrogen bonds : angle 4.73555 / 3.30 ( 946) metal coordination : bond 0.01055 / 0.53 ( 8) metal coordination : angle 2.40785 / 1.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.8668 (tpt) cc_final: 0.8458 (ttt) REVERT: A 343 ASP cc_start: 0.7954 (m-30) cc_final: 0.7483 (m-30) REVERT: A 404 THR cc_start: 0.7227 (m) cc_final: 0.6866 (p) REVERT: A 457 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8004 (ptm-80) REVERT: B 477 ASP cc_start: 0.6509 (p0) cc_final: 0.6030 (m-30) outliers start: 11 outliers final: 7 residues processed: 62 average time/residue: 0.0965 time to fit residues: 7.7482 Evaluate side-chains 58 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 80 GLU Chi-restraints excluded: chain I residue 211 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.086955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.067479 restraints weight = 19917.924| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.99 r_work: 0.3114 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 1.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 6949 Z= 0.172 Angle : 0.656 8.798 9627 Z= 0.356 Chirality : 0.042 0.268 1040 Planarity : 0.004 0.037 1070 Dihedral : 22.345 76.119 1353 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.23 % Allowed : 24.74 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.33), residues: 705 helix: 1.62 (0.31), residues: 274 sheet: -2.07 (0.45), residues: 122 loop : -0.38 (0.38), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 493 TYR 0.035 0.002 TYR B 475 PHE 0.013 0.002 PHE I 86 TRP 0.032 0.002 TRP A 438 HIS 0.004 0.001 HIS I 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 ( 6941) covalent geometry : angle 0.65381 / 0.36 ( 9621) hydrogen bonds : bond 0.04017 / 2.70 ( 347) hydrogen bonds : angle 4.71021 / 3.27 ( 946) metal coordination : bond 0.01316 / 0.68 ( 8) metal coordination : angle 2.14017 / 1.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 278 MET cc_start: 0.8800 (tpt) cc_final: 0.8535 (ttt) REVERT: A 343 ASP cc_start: 0.8141 (m-30) cc_final: 0.7842 (m-30) REVERT: A 404 THR cc_start: 0.7446 (m) cc_final: 0.7088 (p) REVERT: A 446 LYS cc_start: 0.8678 (tppt) cc_final: 0.8366 (tppt) REVERT: A 457 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8066 (ptm-80) REVERT: A 459 ASN cc_start: 0.8833 (t0) cc_final: 0.8323 (t0) REVERT: B 477 ASP cc_start: 0.6510 (p0) cc_final: 0.6043 (m-30) outliers start: 13 outliers final: 8 residues processed: 61 average time/residue: 0.1142 time to fit residues: 8.6889 Evaluate side-chains 56 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 151 TYR Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain I residue 216 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 57 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.086411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.066756 restraints weight = 19869.653| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.05 r_work: 0.3095 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 1.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6949 Z= 0.164 Angle : 0.670 11.239 9627 Z= 0.363 Chirality : 0.043 0.263 1040 Planarity : 0.004 0.034 1070 Dihedral : 22.344 76.351 1353 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.06 % Allowed : 25.60 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.33), residues: 705 helix: 1.65 (0.31), residues: 275 sheet: -2.10 (0.46), residues: 122 loop : -0.30 (0.39), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 89 TYR 0.030 0.002 TYR B 475 PHE 0.029 0.002 PHE A 492 TRP 0.033 0.002 TRP A 438 HIS 0.012 0.002 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 ( 6941) covalent geometry : angle 0.66871 / 0.36 ( 9621) hydrogen bonds : bond 0.03889 / 2.63 ( 347) hydrogen bonds : angle 4.72043 / 3.26 ( 946) metal coordination : bond 0.01343 / 0.68 ( 8) metal coordination : angle 1.84306 / 1.28 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.251 Fit side-chains REVERT: A 278 MET cc_start: 0.8854 (tpt) cc_final: 0.8568 (ttt) REVERT: A 343 ASP cc_start: 0.8171 (m-30) cc_final: 0.7912 (m-30) REVERT: A 404 THR cc_start: 0.7545 (OUTLIER) cc_final: 0.7199 (p) REVERT: A 446 LYS cc_start: 0.8703 (tppt) cc_final: 0.8396 (tppt) REVERT: A 457 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7839 (ptm-80) REVERT: A 459 ASN cc_start: 0.8909 (t0) cc_final: 0.8450 (t0) REVERT: B 477 ASP cc_start: 0.6449 (p0) cc_final: 0.6031 (m-30) REVERT: B 493 ARG cc_start: 0.8678 (mtt90) cc_final: 0.7977 (mpt-90) outliers start: 12 outliers final: 7 residues processed: 55 average time/residue: 0.1199 time to fit residues: 8.1501 Evaluate side-chains 51 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 491 HIS Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 216 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 68 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 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 = 0.3663 r_free = 0.3663 target = 0.086165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.066621 restraints weight = 19631.962| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.00 r_work: 0.3094 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 1.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6949 Z= 0.165 Angle : 0.670 12.424 9627 Z= 0.357 Chirality : 0.043 0.266 1040 Planarity : 0.004 0.033 1070 Dihedral : 22.338 76.452 1353 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.72 % Allowed : 25.43 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.33), residues: 705 helix: 1.66 (0.31), residues: 275 sheet: -2.05 (0.47), residues: 122 loop : -0.34 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 89 TYR 0.033 0.002 TYR B 475 PHE 0.019 0.002 PHE A 492 TRP 0.030 0.002 TRP A 438 HIS 0.007 0.001 HIS A 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 ( 6941) covalent geometry : angle 0.66847 / 0.36 ( 9621) hydrogen bonds : bond 0.03896 / 2.61 ( 347) hydrogen bonds : angle 4.71811 / 3.27 ( 946) metal coordination : bond 0.01323 / 0.68 ( 8) metal coordination : angle 1.70038 / 1.21 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1600.40 seconds wall clock time: 28 minutes 7.79 seconds (1687.79 seconds total)