Starting phenix.real_space_refine on Tue Aug 4 21:29:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9teo_55831/08_2026/9teo_55831.cif Found real_map, /net/cci-nas-00/data/ceres_data/9teo_55831/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9teo_55831/08_2026/9teo_55831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9teo_55831/08_2026/9teo_55831.map" model { file = "/net/cci-nas-00/data/ceres_data/9teo_55831/08_2026/9teo_55831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9teo_55831/08_2026/9teo_55831.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.45, 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: 0.65 Conformation dependent library (CDL) restraints added in 366.1 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: 0.92 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: 1.24 Time building geometry restraints manager: 0.86 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: 3.000 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.060 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.560 ------------------------------------------------------------------------------- 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 : 0.592 9.315 9627 Z= 0.446 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 0.59091 / 0.45 ( 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 : 0.226 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: 0.6715 (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: 0.8268 (mtt90) outliers start: 4 outliers final: 1 residues processed: 157 average time/residue: 0.1059 time to fit residues: 20.8742 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 : 0.234 ------------------------------------------------------------------------------- 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: 7.9990 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 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3675 r_free = 0.3675 target = 0.087504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.069844 restraints weight = 20060.535| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.96 r_work: 0.3164 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.180 6949 Z= 0.355 Angle : 0.990 14.823 9627 Z= 0.541 Chirality : 0.053 0.250 1040 Planarity : 0.009 0.124 1070 Dihedral : 22.740 75.524 1354 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 5.15 % Allowed : 21.99 % 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: -0.40 (0.31), residues: 705 helix: 0.84 (0.30), residues: 267 sheet: -1.47 (0.45), residues: 123 loop : -0.60 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 221 TYR 0.042 0.005 TYR I 238 PHE 0.021 0.003 PHE A 209 TRP 0.046 0.007 TRP A 584 HIS 0.014 0.003 HIS A 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00794 / 0.35 ( 6941) covalent geometry : angle 0.98043 / 0.54 ( 9621) hydrogen bonds : bond 0.06178 / 4.10 ( 347) hydrogen bonds : angle 5.39634 / 3.79 ( 946) metal coordination : bond 0.03236 / 1.80 ( 8) metal coordination : angle 5.46020 / 4.26 ( 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 140 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 SER cc_start: 0.8018 (OUTLIER) cc_final: 0.7814 (p) REVERT: A 368 CYS cc_start: 0.7728 (OUTLIER) cc_final: 0.6907 (p) REVERT: A 468 LEU cc_start: 0.8451 (mt) cc_final: 0.8195 (pp) REVERT: B 471 LEU cc_start: 0.7805 (mt) cc_final: 0.7168 (mt) REVERT: B 475 TYR cc_start: 0.7638 (m-80) cc_final: 0.7284 (m-80) REVERT: B 493 ARG cc_start: 0.8438 (mmt90) cc_final: 0.8121 (mtt90) REVERT: B 501 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8764 (pp) REVERT: I 82 PHE cc_start: 0.7190 (p90) cc_final: 0.6380 (p90) REVERT: I 203 LEU cc_start: 0.7621 (tt) cc_final: 0.6778 (mp) outliers start: 30 outliers final: 7 residues processed: 129 average time/residue: 0.0949 time to fit residues: 16.2985 Evaluate side-chains 98 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 501 LEU 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: 0.9990 chunk 5 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.088032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.069775 restraints weight = 20002.383| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.99 r_work: 0.3171 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.6582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 6949 Z= 0.226 Angle : 0.710 10.387 9627 Z= 0.400 Chirality : 0.045 0.184 1040 Planarity : 0.006 0.044 1070 Dihedral : 22.322 73.130 1353 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.26 % Allowed : 23.71 % 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 (0.32), residues: 705 helix: 1.15 (0.30), residues: 274 sheet: -1.60 (0.43), residues: 133 loop : -0.37 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 551 TYR 0.022 0.002 TYR I 151 PHE 0.018 0.002 PHE I 29 TRP 0.023 0.004 TRP A 220 HIS 0.011 0.002 HIS I 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.23 ( 6941) covalent geometry : angle 0.70474 / 0.40 ( 9621) hydrogen bonds : bond 0.04889 / 3.31 ( 347) hydrogen bonds : angle 5.22055 / 3.64 ( 946) metal coordination : bond 0.03055 / 1.54 ( 8) metal coordination : angle 3.64194 / 3.47 ( 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 110 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 ASP cc_start: 0.6618 (m-30) cc_final: 0.6167 (t70) REVERT: B 471 LEU cc_start: 0.7829 (mt) cc_final: 0.7371 (mt) REVERT: B 475 TYR cc_start: 0.7492 (m-80) cc_final: 0.7277 (m-80) REVERT: B 476 GLU cc_start: 0.7304 (pt0) cc_final: 0.7008 (pt0) REVERT: B 490 LYS cc_start: 0.8320 (tmtt) cc_final: 0.8088 (tmtt) REVERT: B 493 ARG cc_start: 0.8371 (mmt90) cc_final: 0.8159 (mtt90) REVERT: B 501 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8739 (pp) REVERT: I 203 LEU cc_start: 0.7931 (tt) cc_final: 0.6933 (mp) REVERT: I 210 LEU cc_start: 0.6137 (OUTLIER) cc_final: 0.5854 (tt) outliers start: 19 outliers final: 7 residues processed: 106 average time/residue: 0.0865 time to fit residues: 12.0698 Evaluate side-chains 77 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain I residue 42 VAL 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: 0.7980 chunk 9 optimal weight: 0.5980 chunk 50 optimal weight: 7.9990 chunk 7 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.088614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.070108 restraints weight = 20260.823| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.04 r_work: 0.3176 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.7533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6949 Z= 0.178 Angle : 0.664 11.466 9627 Z= 0.367 Chirality : 0.043 0.173 1040 Planarity : 0.005 0.035 1070 Dihedral : 22.429 75.650 1353 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.92 % Allowed : 23.88 % Favored : 73.20 % 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: -0.02 (0.32), residues: 705 helix: 1.50 (0.31), residues: 273 sheet: -1.78 (0.42), residues: 133 loop : -0.47 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 478 TYR 0.012 0.002 TYR I 33 PHE 0.015 0.002 PHE I 183 TRP 0.017 0.002 TRP I 103 HIS 0.006 0.001 HIS I 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 ( 6941) covalent geometry : angle 0.65975 / 0.37 ( 9621) hydrogen bonds : bond 0.04301 / 2.95 ( 347) hydrogen bonds : angle 4.86637 / 3.38 ( 946) metal coordination : bond 0.02483 / 1.49 ( 8) metal coordination : angle 3.17087 / 2.51 ( 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 94 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.238 Fit side-chains REVERT: A 186 ARG cc_start: 0.5484 (ppt170) cc_final: 0.5096 (ptt-90) REVERT: A 343 ASP cc_start: 0.6947 (m-30) cc_final: 0.6573 (t70) REVERT: A 457 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7639 (ptm-80) REVERT: A 468 LEU cc_start: 0.8972 (mt) cc_final: 0.8732 (mp) REVERT: A 478 ARG cc_start: 0.6396 (OUTLIER) cc_final: 0.6047 (tpt170) REVERT: B 493 ARG cc_start: 0.8415 (mmt90) cc_final: 0.8203 (mmt90) REVERT: B 501 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8751 (pp) REVERT: I 210 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6322 (tt) outliers start: 17 outliers final: 8 residues processed: 90 average time/residue: 0.1007 time to fit residues: 11.5347 Evaluate side-chains 75 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain I residue 42 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 65 optimal weight: 0.0570 chunk 7 optimal weight: 0.0980 chunk 4 optimal weight: 7.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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** I 222 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.089143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.070570 restraints weight = 20259.100| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.05 r_work: 0.3195 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.8058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6949 Z= 0.148 Angle : 0.635 10.664 9627 Z= 0.348 Chirality : 0.041 0.191 1040 Planarity : 0.004 0.038 1070 Dihedral : 22.267 75.859 1353 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.09 % Allowed : 24.57 % 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: 0.21 (0.33), residues: 705 helix: 1.79 (0.32), residues: 267 sheet: -1.89 (0.43), residues: 131 loop : -0.29 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 189 TYR 0.021 0.002 TYR I 228 PHE 0.014 0.002 PHE I 173 TRP 0.013 0.002 TRP I 50 HIS 0.003 0.001 HIS A 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 ( 6941) covalent geometry : angle 0.63244 / 0.35 ( 9621) hydrogen bonds : bond 0.03963 / 2.69 ( 347) hydrogen bonds : angle 4.76702 / 3.33 ( 946) metal coordination : bond 0.01538 / 0.92 ( 8) metal coordination : angle 2.30736 / 1.84 ( 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 83 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 ARG cc_start: 0.5382 (ppt170) cc_final: 0.5119 (ptt-90) REVERT: A 343 ASP cc_start: 0.6974 (m-30) cc_final: 0.6596 (t70) REVERT: I 210 LEU cc_start: 0.6521 (OUTLIER) cc_final: 0.6198 (tt) outliers start: 18 outliers final: 11 residues processed: 78 average time/residue: 0.0908 time to fit residues: 9.1918 Evaluate side-chains 72 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ARG 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 A residue 561 ILE Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain I residue 92 VAL 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: 2.9990 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.086966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.067447 restraints weight = 19989.789| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 3.04 r_work: 0.3100 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 1.0274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 6949 Z= 0.263 Angle : 0.773 9.538 9627 Z= 0.424 Chirality : 0.046 0.197 1040 Planarity : 0.007 0.076 1070 Dihedral : 22.621 77.324 1353 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.75 % Allowed : 27.15 % Favored : 70.10 % 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: -0.51 (0.32), residues: 705 helix: 0.99 (0.30), residues: 268 sheet: -2.14 (0.43), residues: 139 loop : -0.50 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG B 493 TYR 0.024 0.003 TYR A 483 PHE 0.024 0.002 PHE A 492 TRP 0.023 0.002 TRP I 50 HIS 0.013 0.002 HIS A 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.26 ( 6941) covalent geometry : angle 0.76746 / 0.42 ( 9621) hydrogen bonds : bond 0.04831 / 3.25 ( 347) hydrogen bonds : angle 4.95163 / 3.43 ( 946) metal coordination : bond 0.03306 / 1.66 ( 8) metal coordination : angle 3.90322 / 2.77 ( 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 76 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.8824 (tpt) cc_final: 0.8530 (tpt) REVERT: A 343 ASP cc_start: 0.8128 (m-30) cc_final: 0.7636 (m-30) REVERT: A 404 THR cc_start: 0.7614 (OUTLIER) cc_final: 0.7177 (p) REVERT: A 446 LYS cc_start: 0.8604 (tppt) cc_final: 0.8334 (tppt) REVERT: A 457 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7933 (ptm-80) REVERT: A 471 LEU cc_start: 0.8197 (mt) cc_final: 0.7932 (mt) REVERT: B 471 LEU cc_start: 0.7315 (mm) cc_final: 0.6325 (mm) REVERT: B 493 ARG cc_start: 0.8597 (mmt90) cc_final: 0.8114 (ptp90) REVERT: B 501 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8683 (pp) outliers start: 16 outliers final: 10 residues processed: 75 average time/residue: 0.0928 time to fit residues: 8.6682 Evaluate side-chains 70 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 501 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 231 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 0.0870 chunk 50 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.087373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.068045 restraints weight = 19811.009| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.98 r_work: 0.3127 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 1.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6949 Z= 0.156 Angle : 0.657 10.410 9627 Z= 0.355 Chirality : 0.042 0.226 1040 Planarity : 0.004 0.031 1070 Dihedral : 22.430 74.943 1353 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.58 % Allowed : 26.98 % Favored : 70.45 % 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 (0.32), residues: 705 helix: 1.54 (0.31), residues: 268 sheet: -2.17 (0.42), residues: 131 loop : -0.49 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 493 TYR 0.037 0.002 TYR B 475 PHE 0.012 0.002 PHE A 209 TRP 0.043 0.002 TRP A 438 HIS 0.005 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 ( 6941) covalent geometry : angle 0.65399 / 0.36 ( 9621) hydrogen bonds : bond 0.03988 / 2.68 ( 347) hydrogen bonds : angle 4.78460 / 3.33 ( 946) metal coordination : bond 0.01547 / 0.79 ( 8) metal coordination : angle 2.47954 / 2.12 ( 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 73 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.203 Fit side-chains REVERT: A 278 MET cc_start: 0.8737 (tpt) cc_final: 0.8451 (tpt) REVERT: A 308 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7886 (mt-10) REVERT: A 343 ASP cc_start: 0.7988 (m-30) cc_final: 0.7518 (m-30) REVERT: A 404 THR cc_start: 0.7360 (OUTLIER) cc_final: 0.6988 (p) REVERT: A 446 LYS cc_start: 0.8578 (tppt) cc_final: 0.8360 (tppt) REVERT: A 457 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7841 (ptm-80) outliers start: 15 outliers final: 7 residues processed: 71 average time/residue: 0.0950 time to fit residues: 8.5377 Evaluate side-chains 59 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 558 VAL 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 231 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 0.0040 chunk 56 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.086892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.067474 restraints weight = 19788.589| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.00 r_work: 0.3112 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 1.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 6949 Z= 0.167 Angle : 0.652 10.899 9627 Z= 0.360 Chirality : 0.042 0.168 1040 Planarity : 0.004 0.030 1070 Dihedral : 22.332 75.362 1353 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.58 % Allowed : 27.15 % Favored : 70.27 % 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: -0.00 (0.33), residues: 705 helix: 1.63 (0.32), residues: 269 sheet: -2.09 (0.45), residues: 125 loop : -0.44 (0.38), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 172 TYR 0.036 0.002 TYR B 475 PHE 0.014 0.001 PHE A 492 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 0.00346 / 0.17 ( 6941) covalent geometry : angle 0.65039 / 0.36 ( 9621) hydrogen bonds : bond 0.03951 / 2.68 ( 347) hydrogen bonds : angle 4.65398 / 3.25 ( 946) metal coordination : bond 0.01484 / 0.75 ( 8) metal coordination : angle 2.13910 / 1.63 ( 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: 15 poor density : 50 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.8819 (tpt) cc_final: 0.8546 (tpt) REVERT: A 334 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7894 (pm20) REVERT: A 343 ASP cc_start: 0.8108 (m-30) cc_final: 0.7838 (m-30) REVERT: A 404 THR cc_start: 0.7478 (OUTLIER) cc_final: 0.7113 (p) REVERT: A 446 LYS cc_start: 0.8649 (tppt) cc_final: 0.8363 (tppt) REVERT: A 457 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8040 (ptm-80) REVERT: A 459 ASN cc_start: 0.8871 (t0) cc_final: 0.8469 (t0) REVERT: B 477 ASP cc_start: 0.6405 (p0) cc_final: 0.6087 (m-30) REVERT: B 493 ARG cc_start: 0.8679 (mmt90) cc_final: 0.8157 (ptp90) outliers start: 15 outliers final: 8 residues processed: 61 average time/residue: 0.1027 time to fit residues: 7.8718 Evaluate side-chains 57 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 404 THR 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 80 GLU Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 151 TYR Chi-restraints excluded: chain I residue 172 ARG Chi-restraints excluded: chain I residue 231 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3653 r_free = 0.3653 target = 0.085945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.066361 restraints weight = 19775.579| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.99 r_work: 0.3088 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 1.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6949 Z= 0.172 Angle : 0.651 10.525 9627 Z= 0.355 Chirality : 0.042 0.230 1040 Planarity : 0.004 0.035 1070 Dihedral : 22.324 75.783 1353 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.23 % Allowed : 27.66 % Favored : 70.10 % 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: -0.02 (0.33), residues: 705 helix: 1.61 (0.31), residues: 269 sheet: -2.20 (0.43), residues: 137 loop : -0.29 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 493 TYR 0.031 0.002 TYR B 475 PHE 0.028 0.002 PHE A 492 TRP 0.053 0.002 TRP A 438 HIS 0.004 0.001 HIS A 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 ( 6941) covalent geometry : angle 0.64926 / 0.35 ( 9621) hydrogen bonds : bond 0.03972 / 2.65 ( 347) hydrogen bonds : angle 4.69515 / 3.25 ( 946) metal coordination : bond 0.01457 / 0.74 ( 8) metal coordination : angle 1.86843 / 1.36 ( 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 60 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.8920 (tpt) cc_final: 0.8625 (tpt) REVERT: A 343 ASP cc_start: 0.8177 (m-30) cc_final: 0.7955 (m-30) REVERT: A 404 THR cc_start: 0.7696 (OUTLIER) cc_final: 0.7379 (p) REVERT: A 446 LYS cc_start: 0.8693 (tppt) cc_final: 0.8402 (tppt) REVERT: A 457 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8084 (ptm-80) REVERT: A 459 ASN cc_start: 0.8993 (t0) cc_final: 0.8599 (t0) REVERT: B 477 ASP cc_start: 0.6707 (p0) cc_final: 0.6358 (m-30) REVERT: I 130 MET cc_start: 0.5794 (ppp) cc_final: 0.5453 (ppp) outliers start: 13 outliers final: 5 residues processed: 58 average time/residue: 0.1063 time to fit residues: 7.7232 Evaluate side-chains 49 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 THR 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 92 VAL Chi-restraints excluded: chain I residue 151 TYR Chi-restraints excluded: chain I residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 57 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 21 optimal weight: 0.0670 chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.086023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.066476 restraints weight = 19648.290| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.98 r_work: 0.3091 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 1.2137 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= 0.155 Angle : 0.636 8.100 9627 Z= 0.348 Chirality : 0.042 0.216 1040 Planarity : 0.004 0.033 1070 Dihedral : 22.267 75.906 1353 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.89 % Allowed : 27.49 % Favored : 70.62 % 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: 0.02 (0.33), residues: 705 helix: 1.69 (0.32), residues: 269 sheet: -2.33 (0.47), residues: 121 loop : -0.38 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 442 TYR 0.031 0.002 TYR B 475 PHE 0.010 0.001 PHE A 209 TRP 0.039 0.002 TRP A 438 HIS 0.003 0.001 HIS A 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 ( 6941) covalent geometry : angle 0.63510 / 0.35 ( 9621) hydrogen bonds : bond 0.03853 / 2.60 ( 347) hydrogen bonds : angle 4.62858 / 3.22 ( 946) metal coordination : bond 0.01289 / 0.65 ( 8) metal coordination : angle 1.74255 / 1.32 ( 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 54 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.179 Fit side-chains REVERT: A 278 MET cc_start: 0.8951 (tpt) cc_final: 0.8645 (tpt) REVERT: A 343 ASP cc_start: 0.8245 (m-30) cc_final: 0.7994 (m-30) REVERT: A 404 THR cc_start: 0.7678 (OUTLIER) cc_final: 0.7344 (p) REVERT: A 457 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7919 (ptm-80) REVERT: A 459 ASN cc_start: 0.9036 (t0) cc_final: 0.8654 (t0) REVERT: B 477 ASP cc_start: 0.6633 (p0) cc_final: 0.6352 (m-30) outliers start: 11 outliers final: 7 residues processed: 50 average time/residue: 0.1130 time to fit residues: 6.9545 Evaluate side-chains 49 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 404 THR 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 92 VAL Chi-restraints excluded: chain I residue 151 TYR Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 68 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 HIS ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.086482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.067038 restraints weight = 19494.034| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.90 r_work: 0.3130 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 1.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6949 Z= 0.171 Angle : 0.650 8.655 9627 Z= 0.354 Chirality : 0.043 0.236 1040 Planarity : 0.004 0.037 1070 Dihedral : 22.302 76.242 1353 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.55 % Allowed : 28.18 % Favored : 70.27 % 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: 0.09 (0.33), residues: 705 helix: 1.64 (0.32), residues: 269 sheet: -2.18 (0.51), residues: 100 loop : -0.45 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 493 TYR 0.030 0.002 TYR B 475 PHE 0.023 0.002 PHE A 492 TRP 0.043 0.002 TRP A 438 HIS 0.004 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 ( 6941) covalent geometry : angle 0.64866 / 0.35 ( 9621) hydrogen bonds : bond 0.03985 / 2.69 ( 347) hydrogen bonds : angle 4.64337 / 3.23 ( 946) metal coordination : bond 0.01522 / 0.76 ( 8) metal coordination : angle 1.65819 / 1.07 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1583.10 seconds wall clock time: 27 minutes 43.10 seconds (1663.10 seconds total)