Starting phenix.real_space_refine on Tue Mar 3 17:27:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8by6_16321/03_2026/8by6_16321.cif Found real_map, /net/cci-nas-00/data/ceres_data/8by6_16321/03_2026/8by6_16321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8by6_16321/03_2026/8by6_16321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8by6_16321/03_2026/8by6_16321.map" model { file = "/net/cci-nas-00/data/ceres_data/8by6_16321/03_2026/8by6_16321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8by6_16321/03_2026/8by6_16321.cif" } resolution = 3.19 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 44 5.16 5 C 4842 2.51 5 N 1307 2.21 5 O 1405 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7601 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 6120 Classifications: {'peptide': 748} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 707} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1237 Classifications: {'peptide': 152} Link IDs: {'TRANS': 151} Chain: "C" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 192 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'GTG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.76, per 1000 atoms: 0.23 Number of scatterers: 7601 At special positions: 0 Unit cell: (103.375, 91.797, 113.299, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 3 15.00 O 1405 8.00 N 1307 7.00 C 4842 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: 0.76 Conformation dependent library (CDL) restraints added in 274.2 milliseconds 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1778 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 1 sheets defined 72.7% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 25 through 38 removed outlier: 3.921A pdb=" N VAL A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 60 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 64 through 79 Processing helix chain 'A' and resid 82 through 95 Processing helix chain 'A' and resid 97 through 118 Processing helix chain 'A' and resid 121 through 137 removed outlier: 4.077A pdb=" N ASN A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 155 removed outlier: 3.515A pdb=" N MET A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 162 through 205 removed outlier: 3.782A pdb=" N ARG A 166 " --> pdb=" O PRO A 162 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 6.307A pdb=" N LYS A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ALA A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLU A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 removed outlier: 3.507A pdb=" N LEU A 214 " --> pdb=" O HIS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 242 Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.578A pdb=" N GLU A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 308 through 325 removed outlier: 3.540A pdb=" N PHE A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 346 through 361 Processing helix chain 'A' and resid 368 through 383 removed outlier: 3.588A pdb=" N TYR A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 401 Processing helix chain 'A' and resid 402 through 405 Processing helix chain 'A' and resid 406 through 424 Processing helix chain 'A' and resid 429 through 433 Processing helix chain 'A' and resid 434 through 439 removed outlier: 4.296A pdb=" N SER A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN A 439 " --> pdb=" O ASP A 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 434 through 439' Processing helix chain 'A' and resid 443 through 459 Processing helix chain 'A' and resid 461 through 467 removed outlier: 3.582A pdb=" N ILE A 465 " --> pdb=" O TYR A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 477 removed outlier: 4.547A pdb=" N ALA A 475 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 513 through 522 Processing helix chain 'A' and resid 540 through 555 Processing helix chain 'A' and resid 558 through 569 Processing helix chain 'A' and resid 569 through 577 Processing helix chain 'A' and resid 579 through 594 Processing helix chain 'A' and resid 597 through 611 Processing helix chain 'A' and resid 615 through 624 removed outlier: 3.533A pdb=" N PHE A 624 " --> pdb=" O ALA A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 634 through 676 removed outlier: 3.977A pdb=" N TRP A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP A 676 " --> pdb=" O ARG A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 732 Processing helix chain 'A' and resid 737 through 754 Processing helix chain 'A' and resid 754 through 769 removed outlier: 4.961A pdb=" N GLN A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TYR A 761 " --> pdb=" O ILE A 757 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N VAL A 763 " --> pdb=" O GLN A 759 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N THR A 764 " --> pdb=" O GLN A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 789 removed outlier: 4.057A pdb=" N VAL A 781 " --> pdb=" O HIS A 777 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 782 " --> pdb=" O ILE A 778 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN A 789 " --> pdb=" O PHE A 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 11 Processing helix chain 'B' and resid 28 through 39 removed outlier: 3.728A pdb=" N LYS B 38 " --> pdb=" O LYS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 62 removed outlier: 3.704A pdb=" N ILE B 56 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 101 removed outlier: 3.566A pdb=" N ALA B 94 " --> pdb=" O SER B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 139 Processing helix chain 'B' and resid 143 through 147 Processing helix chain 'B' and resid 150 through 155 removed outlier: 3.790A pdb=" N GLN B 154 " --> pdb=" O GLY B 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 594 Processing sheet with id=AA1, first strand: chain 'B' and resid 66 through 73 removed outlier: 5.259A pdb=" N ILE B 66 " --> pdb=" O GLU B 87 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLU B 87 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS B 68 " --> pdb=" O PHE B 85 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE B 85 " --> pdb=" O LYS B 68 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE B 70 " --> pdb=" O PHE B 83 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N PHE B 83 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N GLY B 72 " --> pdb=" O CYS B 81 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1330 1.32 - 1.44: 2027 1.44 - 1.57: 4352 1.57 - 1.69: 6 1.69 - 1.81: 66 Bond restraints: 7781 Sorted by residual: bond pdb=" C5A GTG B 201 " pdb=" C6A GTG B 201 " ideal model delta sigma weight residual 1.427 1.330 0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C5B GTG B 201 " pdb=" C6B GTG B 201 " ideal model delta sigma weight residual 1.424 1.331 0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C1D GTG B 201 " pdb=" O4D GTG B 201 " ideal model delta sigma weight residual 1.383 1.466 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C1E GTG B 201 " pdb=" O4E GTG B 201 " ideal model delta sigma weight residual 1.392 1.473 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C PRO A 470 " pdb=" O PRO A 470 " ideal model delta sigma weight residual 1.240 1.204 0.036 1.12e-02 7.97e+03 1.03e+01 ... (remaining 7776 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 10236 1.99 - 3.98: 250 3.98 - 5.98: 34 5.98 - 7.97: 10 7.97 - 9.96: 4 Bond angle restraints: 10534 Sorted by residual: angle pdb=" CA ASP A 29 " pdb=" CB ASP A 29 " pdb=" CG ASP A 29 " ideal model delta sigma weight residual 112.60 118.25 -5.65 1.00e+00 1.00e+00 3.19e+01 angle pdb=" C GLU A 26 " pdb=" CA GLU A 26 " pdb=" CB GLU A 26 " ideal model delta sigma weight residual 110.96 117.98 -7.02 1.54e+00 4.22e-01 2.08e+01 angle pdb=" C ASP A 29 " pdb=" CA ASP A 29 " pdb=" CB ASP A 29 " ideal model delta sigma weight residual 110.81 117.87 -7.06 1.60e+00 3.91e-01 1.95e+01 angle pdb=" N GLU A 26 " pdb=" CA GLU A 26 " pdb=" C GLU A 26 " ideal model delta sigma weight residual 110.97 106.44 4.53 1.09e+00 8.42e-01 1.73e+01 angle pdb=" C SER A 33 " pdb=" N LEU A 34 " pdb=" CA LEU A 34 " ideal model delta sigma weight residual 120.54 125.16 -4.62 1.35e+00 5.49e-01 1.17e+01 ... (remaining 10529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.94: 4294 26.94 - 53.87: 396 53.87 - 80.81: 47 80.81 - 107.74: 5 107.74 - 134.68: 1 Dihedral angle restraints: 4743 sinusoidal: 2013 harmonic: 2730 Sorted by residual: dihedral pdb=" O5D GTG B 201 " pdb=" O3A GTG B 201 " pdb=" PA GTG B 201 " pdb=" PB GTG B 201 " ideal model delta sinusoidal sigma weight residual -105.71 28.97 -134.68 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" CA ASP B 114 " pdb=" CB ASP B 114 " pdb=" CG ASP B 114 " pdb=" OD1 ASP B 114 " ideal model delta sinusoidal sigma weight residual -30.00 -88.39 58.39 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASP A 369 " pdb=" CB ASP A 369 " pdb=" CG ASP A 369 " pdb=" OD1 ASP A 369 " ideal model delta sinusoidal sigma weight residual -30.00 -88.27 58.27 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 4740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 945 0.046 - 0.092: 147 0.092 - 0.138: 45 0.138 - 0.183: 4 0.183 - 0.229: 3 Chirality restraints: 1144 Sorted by residual: chirality pdb=" C4E GTG B 201 " pdb=" C3E GTG B 201 " pdb=" C5E GTG B 201 " pdb=" O4E GTG B 201 " both_signs ideal model delta sigma weight residual False -2.55 -2.78 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C4D GTG B 201 " pdb=" C3D GTG B 201 " pdb=" C5D GTG B 201 " pdb=" O4D GTG B 201 " both_signs ideal model delta sigma weight residual False -2.52 -2.75 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA THR A 88 " pdb=" N THR A 88 " pdb=" C THR A 88 " pdb=" CB THR A 88 " both_signs ideal model delta sigma weight residual False 2.53 2.71 -0.18 2.00e-01 2.50e+01 8.51e-01 ... (remaining 1141 not shown) Planarity restraints: 1345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 61 " -0.050 5.00e-02 4.00e+02 7.36e-02 8.66e+00 pdb=" N PRO A 62 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 62 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 62 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 258 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.99e+00 pdb=" C SER A 258 " -0.039 2.00e-02 2.50e+03 pdb=" O SER A 258 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE A 259 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 461 " 0.021 2.00e-02 2.50e+03 1.32e-02 3.50e+00 pdb=" CG TYR A 461 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR A 461 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 461 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 461 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 461 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 461 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 461 " 0.003 2.00e-02 2.50e+03 ... (remaining 1342 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 84 2.62 - 3.19: 6883 3.19 - 3.76: 12195 3.76 - 4.33: 16291 4.33 - 4.90: 27567 Nonbonded interactions: 63020 Sorted by model distance: nonbonded pdb=" OE2 GLU A 32 " pdb=" CG LYS B 7 " model vdw 2.044 3.440 nonbonded pdb=" O SER B 63 " pdb=" OG SER B 63 " model vdw 2.221 3.040 nonbonded pdb=" OD2 ASP A 167 " pdb=" NH2 ARG A 206 " model vdw 2.229 3.120 nonbonded pdb=" OH TYR B 20 " pdb=" O2D GTG B 201 " model vdw 2.268 3.040 nonbonded pdb=" O ILE A 414 " pdb=" OG SER A 418 " model vdw 2.282 3.040 ... (remaining 63015 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: 1.850 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.390 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:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 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 : 0.005 0.097 7781 Z= 0.264 Angle : 0.719 9.959 10534 Z= 0.394 Chirality : 0.040 0.229 1144 Planarity : 0.004 0.074 1345 Dihedral : 18.826 134.677 2965 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.88 % Allowed : 27.73 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.38 (0.28), residues: 913 helix: 2.33 (0.22), residues: 594 sheet: -1.19 (1.23), residues: 11 loop : 0.25 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 464 TYR 0.029 0.001 TYR A 461 PHE 0.008 0.001 PHE A 473 TRP 0.009 0.001 TRP A 416 HIS 0.013 0.001 HIS A 570 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 7781) covalent geometry : angle 0.71913 (10534) hydrogen bonds : bond 0.11732 ( 458) hydrogen bonds : angle 4.73119 ( 1326) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7472 (p0) REVERT: A 648 MET cc_start: 0.8727 (tpp) cc_final: 0.8514 (tpt) outliers start: 24 outliers final: 11 residues processed: 147 average time/residue: 0.0907 time to fit residues: 17.8094 Evaluate side-chains 99 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 701 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.0470 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 317 ASN A 561 HIS A 753 GLN B 55 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.078047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.058174 restraints weight = 19178.984| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.31 r_work: 0.2658 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7781 Z= 0.151 Angle : 0.567 7.442 10534 Z= 0.290 Chirality : 0.040 0.159 1144 Planarity : 0.004 0.045 1345 Dihedral : 7.285 130.076 1082 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.88 % Allowed : 26.17 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.71 (0.28), residues: 913 helix: 2.57 (0.21), residues: 611 sheet: -0.71 (1.24), residues: 11 loop : 0.24 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 112 TYR 0.013 0.001 TYR A 86 PHE 0.020 0.001 PHE B 25 TRP 0.010 0.001 TRP A 168 HIS 0.007 0.001 HIS A 570 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 7781) covalent geometry : angle 0.56679 (10534) hydrogen bonds : bond 0.03915 ( 458) hydrogen bonds : angle 3.79951 ( 1326) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7809 (p0) REVERT: A 114 GLU cc_start: 0.9245 (tt0) cc_final: 0.8784 (tm-30) REVERT: A 133 ASP cc_start: 0.9596 (t70) cc_final: 0.9262 (t70) REVERT: A 220 ASP cc_start: 0.8693 (p0) cc_final: 0.8422 (p0) REVERT: A 316 GLU cc_start: 0.8386 (tp30) cc_final: 0.8180 (tp30) REVERT: B 46 ASN cc_start: 0.9170 (t0) cc_final: 0.8872 (t0) REVERT: B 54 GLU cc_start: 0.9147 (mp0) cc_final: 0.8862 (mp0) REVERT: B 81 CYS cc_start: 0.8736 (t) cc_final: 0.8128 (m) REVERT: B 116 ASP cc_start: 0.8801 (t0) cc_final: 0.8325 (t70) REVERT: B 121 GLU cc_start: 0.9299 (mm-30) cc_final: 0.9011 (tp30) outliers start: 24 outliers final: 12 residues processed: 102 average time/residue: 0.0913 time to fit residues: 12.5620 Evaluate side-chains 95 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 585 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 30 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN ** A 540 ASN ** 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 = 0.3263 r_free = 0.3263 target = 0.077331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.056559 restraints weight = 19549.752| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.42 r_work: 0.2632 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7781 Z= 0.150 Angle : 0.524 7.344 10534 Z= 0.267 Chirality : 0.039 0.167 1144 Planarity : 0.004 0.047 1345 Dihedral : 6.712 124.514 1073 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.12 % Allowed : 26.29 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.85 (0.28), residues: 913 helix: 2.68 (0.21), residues: 610 sheet: -0.55 (1.27), residues: 11 loop : 0.30 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 112 TYR 0.017 0.001 TYR A 86 PHE 0.014 0.001 PHE A 569 TRP 0.010 0.001 TRP A 638 HIS 0.004 0.001 HIS A 570 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 7781) covalent geometry : angle 0.52392 (10534) hydrogen bonds : bond 0.03703 ( 458) hydrogen bonds : angle 3.66006 ( 1326) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9164 (tpp) cc_final: 0.8818 (tpp) REVERT: A 114 GLU cc_start: 0.9243 (tt0) cc_final: 0.8838 (tm-30) REVERT: A 133 ASP cc_start: 0.9552 (t70) cc_final: 0.9208 (t70) REVERT: A 200 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8354 (tm-30) REVERT: A 220 ASP cc_start: 0.8782 (p0) cc_final: 0.8447 (p0) REVERT: A 316 GLU cc_start: 0.8611 (tp30) cc_final: 0.8367 (tp30) REVERT: B 31 GLU cc_start: 0.9113 (tm-30) cc_final: 0.8891 (tm-30) REVERT: B 46 ASN cc_start: 0.9206 (t0) cc_final: 0.8853 (t0) REVERT: B 81 CYS cc_start: 0.8771 (t) cc_final: 0.8039 (m) REVERT: B 110 ILE cc_start: 0.9386 (mm) cc_final: 0.9151 (mm) REVERT: B 116 ASP cc_start: 0.8855 (t0) cc_final: 0.8554 (t70) outliers start: 26 outliers final: 13 residues processed: 106 average time/residue: 0.0948 time to fit residues: 13.3017 Evaluate side-chains 95 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 585 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 29 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 83 optimal weight: 0.0970 chunk 4 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.077306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.057005 restraints weight = 19664.518| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 3.40 r_work: 0.2651 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7781 Z= 0.123 Angle : 0.513 7.435 10534 Z= 0.259 Chirality : 0.038 0.162 1144 Planarity : 0.004 0.046 1345 Dihedral : 6.393 120.733 1071 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.12 % Allowed : 26.29 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.93 (0.28), residues: 913 helix: 2.71 (0.21), residues: 611 sheet: -0.43 (1.26), residues: 11 loop : 0.40 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 10 TYR 0.009 0.001 TYR A 461 PHE 0.014 0.001 PHE A 569 TRP 0.009 0.001 TRP A 416 HIS 0.004 0.001 HIS A 754 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7781) covalent geometry : angle 0.51297 (10534) hydrogen bonds : bond 0.03403 ( 458) hydrogen bonds : angle 3.55966 ( 1326) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.9258 (m) cc_final: 0.8936 (t) REVERT: A 108 MET cc_start: 0.9152 (tpp) cc_final: 0.8943 (tpp) REVERT: A 114 GLU cc_start: 0.9211 (tt0) cc_final: 0.8845 (tm-30) REVERT: A 133 ASP cc_start: 0.9501 (t70) cc_final: 0.8831 (t70) REVERT: A 200 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8334 (tm-30) REVERT: A 220 ASP cc_start: 0.8832 (p0) cc_final: 0.8455 (p0) REVERT: A 261 CYS cc_start: 0.9279 (t) cc_final: 0.9052 (p) REVERT: A 316 GLU cc_start: 0.8627 (tp30) cc_final: 0.8366 (tp30) REVERT: B 46 ASN cc_start: 0.9198 (t0) cc_final: 0.8861 (t0) REVERT: B 81 CYS cc_start: 0.8771 (t) cc_final: 0.8031 (m) REVERT: B 110 ILE cc_start: 0.9388 (mm) cc_final: 0.9147 (mm) REVERT: B 116 ASP cc_start: 0.8850 (t0) cc_final: 0.8574 (t70) outliers start: 26 outliers final: 12 residues processed: 107 average time/residue: 0.0929 time to fit residues: 13.5420 Evaluate side-chains 92 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 585 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 6 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 498 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.075334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.054643 restraints weight = 19849.436| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 3.44 r_work: 0.2599 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7781 Z= 0.195 Angle : 0.544 7.680 10534 Z= 0.276 Chirality : 0.040 0.153 1144 Planarity : 0.004 0.045 1345 Dihedral : 6.399 119.377 1069 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.00 % Allowed : 26.65 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.95 (0.28), residues: 913 helix: 2.73 (0.21), residues: 608 sheet: -0.19 (1.34), residues: 11 loop : 0.43 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 10 TYR 0.010 0.001 TYR A 202 PHE 0.011 0.001 PHE A 569 TRP 0.010 0.001 TRP A 638 HIS 0.004 0.001 HIS A 754 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 7781) covalent geometry : angle 0.54407 (10534) hydrogen bonds : bond 0.03767 ( 458) hydrogen bonds : angle 3.66916 ( 1326) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.9250 (m) cc_final: 0.8877 (t) REVERT: A 108 MET cc_start: 0.9188 (tpp) cc_final: 0.8897 (tpp) REVERT: A 114 GLU cc_start: 0.9242 (tt0) cc_final: 0.8877 (tm-30) REVERT: A 133 ASP cc_start: 0.9504 (t70) cc_final: 0.8841 (t70) REVERT: A 200 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8377 (tm-30) REVERT: A 207 GLN cc_start: 0.9245 (OUTLIER) cc_final: 0.8767 (mp10) REVERT: A 220 ASP cc_start: 0.8864 (p0) cc_final: 0.8514 (p0) REVERT: A 225 GLN cc_start: 0.9303 (OUTLIER) cc_final: 0.8187 (mp-120) REVERT: A 261 CYS cc_start: 0.9294 (t) cc_final: 0.9062 (p) REVERT: A 316 GLU cc_start: 0.8752 (tp30) cc_final: 0.8489 (tp30) REVERT: B 46 ASN cc_start: 0.9226 (t0) cc_final: 0.8869 (t0) REVERT: B 81 CYS cc_start: 0.8890 (t) cc_final: 0.8117 (m) REVERT: B 110 ILE cc_start: 0.9410 (mm) cc_final: 0.9191 (mm) REVERT: B 116 ASP cc_start: 0.8874 (t0) cc_final: 0.8589 (t70) REVERT: B 129 ARG cc_start: 0.8940 (ptm-80) cc_final: 0.8714 (ttp80) outliers start: 25 outliers final: 14 residues processed: 106 average time/residue: 0.0911 time to fit residues: 13.1238 Evaluate side-chains 94 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 585 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 14 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 39 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 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 = 0.3251 r_free = 0.3251 target = 0.076449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.055841 restraints weight = 19834.569| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 3.46 r_work: 0.2628 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7781 Z= 0.130 Angle : 0.524 8.141 10534 Z= 0.265 Chirality : 0.038 0.142 1144 Planarity : 0.004 0.044 1345 Dihedral : 6.247 118.350 1069 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.52 % Allowed : 27.61 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.01 (0.28), residues: 913 helix: 2.74 (0.21), residues: 609 sheet: -0.21 (1.33), residues: 11 loop : 0.51 (0.38), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 10 TYR 0.015 0.001 TYR A 86 PHE 0.013 0.001 PHE A 569 TRP 0.010 0.001 TRP A 416 HIS 0.004 0.001 HIS A 754 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7781) covalent geometry : angle 0.52448 (10534) hydrogen bonds : bond 0.03470 ( 458) hydrogen bonds : angle 3.57884 ( 1326) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 87 THR cc_start: 0.9243 (m) cc_final: 0.8889 (t) REVERT: A 108 MET cc_start: 0.9166 (tpp) cc_final: 0.8869 (tpp) REVERT: A 114 GLU cc_start: 0.9238 (tt0) cc_final: 0.8872 (tm-30) REVERT: A 133 ASP cc_start: 0.9470 (t70) cc_final: 0.8692 (t70) REVERT: A 200 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8342 (tm-30) REVERT: A 207 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8723 (mp10) REVERT: A 220 ASP cc_start: 0.8838 (p0) cc_final: 0.8427 (p0) REVERT: A 261 CYS cc_start: 0.9280 (t) cc_final: 0.9065 (p) REVERT: A 316 GLU cc_start: 0.8710 (tp30) cc_final: 0.8444 (tp30) REVERT: B 46 ASN cc_start: 0.9198 (t0) cc_final: 0.8830 (t0) REVERT: B 81 CYS cc_start: 0.8908 (t) cc_final: 0.8087 (m) REVERT: B 110 ILE cc_start: 0.9388 (mm) cc_final: 0.9155 (mm) REVERT: B 129 ARG cc_start: 0.8891 (ptm-80) cc_final: 0.8671 (ttp80) outliers start: 21 outliers final: 12 residues processed: 107 average time/residue: 0.1124 time to fit residues: 15.6099 Evaluate side-chains 91 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 585 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 74 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN ** B 32 GLN ** 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 = 0.3226 r_free = 0.3226 target = 0.075174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.055627 restraints weight = 19690.384| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 3.30 r_work: 0.2620 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7781 Z= 0.172 Angle : 0.557 7.566 10534 Z= 0.279 Chirality : 0.039 0.136 1144 Planarity : 0.005 0.079 1345 Dihedral : 6.251 117.669 1069 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.40 % Allowed : 27.25 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.97 (0.28), residues: 913 helix: 2.70 (0.21), residues: 608 sheet: 0.09 (1.42), residues: 11 loop : 0.52 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 668 TYR 0.015 0.001 TYR A 86 PHE 0.012 0.001 PHE A 569 TRP 0.009 0.001 TRP A 638 HIS 0.004 0.001 HIS A 754 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 7781) covalent geometry : angle 0.55710 (10534) hydrogen bonds : bond 0.03569 ( 458) hydrogen bonds : angle 3.60368 ( 1326) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 87 THR cc_start: 0.9232 (m) cc_final: 0.8848 (t) REVERT: A 108 MET cc_start: 0.9182 (tpp) cc_final: 0.8767 (tpp) REVERT: A 114 GLU cc_start: 0.9228 (tt0) cc_final: 0.8874 (tm-30) REVERT: A 133 ASP cc_start: 0.9453 (t70) cc_final: 0.8676 (t70) REVERT: A 200 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8364 (tm-30) REVERT: A 207 GLN cc_start: 0.9229 (OUTLIER) cc_final: 0.8738 (mp10) REVERT: A 220 ASP cc_start: 0.8849 (p0) cc_final: 0.8502 (p0) REVERT: A 225 GLN cc_start: 0.9298 (OUTLIER) cc_final: 0.8522 (mp-120) REVERT: A 316 GLU cc_start: 0.8766 (tp30) cc_final: 0.8494 (tp30) REVERT: B 46 ASN cc_start: 0.9203 (t0) cc_final: 0.8838 (t0) REVERT: B 81 CYS cc_start: 0.8944 (t) cc_final: 0.8133 (m) REVERT: B 110 ILE cc_start: 0.9400 (mm) cc_final: 0.9180 (mm) REVERT: B 129 ARG cc_start: 0.8903 (ptm-80) cc_final: 0.8690 (ttp80) REVERT: B 141 ASP cc_start: 0.9149 (t0) cc_final: 0.8893 (p0) outliers start: 20 outliers final: 14 residues processed: 93 average time/residue: 0.0954 time to fit residues: 11.9458 Evaluate side-chains 91 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 585 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 25 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 chunk 73 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 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 = 0.3262 r_free = 0.3262 target = 0.076907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.056481 restraints weight = 19792.433| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 3.45 r_work: 0.2640 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7781 Z= 0.116 Angle : 0.532 7.582 10534 Z= 0.268 Chirality : 0.038 0.135 1144 Planarity : 0.004 0.043 1345 Dihedral : 5.982 115.694 1066 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.52 % Allowed : 26.65 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.00 (0.28), residues: 913 helix: 2.71 (0.21), residues: 609 sheet: -0.02 (1.40), residues: 11 loop : 0.57 (0.39), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 10 TYR 0.015 0.001 TYR A 86 PHE 0.013 0.001 PHE A 569 TRP 0.010 0.001 TRP A 416 HIS 0.004 0.001 HIS A 754 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7781) covalent geometry : angle 0.53189 (10534) hydrogen bonds : bond 0.03325 ( 458) hydrogen bonds : angle 3.52029 ( 1326) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 108 MET cc_start: 0.9161 (tpp) cc_final: 0.8758 (tpp) REVERT: A 114 GLU cc_start: 0.9230 (tt0) cc_final: 0.8869 (tm-30) REVERT: A 133 ASP cc_start: 0.9427 (t70) cc_final: 0.9038 (t70) REVERT: A 200 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8323 (tm-30) REVERT: A 207 GLN cc_start: 0.9228 (OUTLIER) cc_final: 0.8777 (mp10) REVERT: A 220 ASP cc_start: 0.8867 (p0) cc_final: 0.8468 (p0) REVERT: A 316 GLU cc_start: 0.8722 (tp30) cc_final: 0.8462 (tp30) REVERT: A 694 ARG cc_start: 0.9101 (mmm-85) cc_final: 0.8896 (mmm-85) REVERT: B 46 ASN cc_start: 0.9172 (t0) cc_final: 0.8807 (t0) REVERT: B 81 CYS cc_start: 0.8929 (t) cc_final: 0.8074 (m) REVERT: B 110 ILE cc_start: 0.9379 (mm) cc_final: 0.9149 (mm) REVERT: B 129 ARG cc_start: 0.8867 (ptm-80) cc_final: 0.8662 (ttp80) REVERT: B 141 ASP cc_start: 0.9131 (t0) cc_final: 0.8924 (p0) outliers start: 21 outliers final: 13 residues processed: 93 average time/residue: 0.0946 time to fit residues: 11.9055 Evaluate side-chains 92 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 585 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 23 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 73 optimal weight: 0.1980 chunk 15 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 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 = 0.3269 r_free = 0.3269 target = 0.077199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.056764 restraints weight = 19775.080| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 3.45 r_work: 0.2650 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7781 Z= 0.119 Angle : 0.533 8.063 10534 Z= 0.269 Chirality : 0.038 0.139 1144 Planarity : 0.004 0.043 1345 Dihedral : 5.851 111.650 1066 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.92 % Allowed : 27.85 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.04 (0.28), residues: 913 helix: 2.73 (0.21), residues: 610 sheet: 0.02 (1.41), residues: 11 loop : 0.61 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 668 TYR 0.021 0.001 TYR A 399 PHE 0.012 0.001 PHE A 569 TRP 0.009 0.001 TRP A 638 HIS 0.004 0.001 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 7781) covalent geometry : angle 0.53288 (10534) hydrogen bonds : bond 0.03247 ( 458) hydrogen bonds : angle 3.51149 ( 1326) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 108 MET cc_start: 0.9172 (tpp) cc_final: 0.8784 (tpp) REVERT: A 114 GLU cc_start: 0.9235 (tt0) cc_final: 0.8875 (tm-30) REVERT: A 133 ASP cc_start: 0.9409 (t70) cc_final: 0.9036 (t70) REVERT: A 200 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8309 (tm-30) REVERT: A 207 GLN cc_start: 0.9230 (OUTLIER) cc_final: 0.8826 (mp10) REVERT: A 220 ASP cc_start: 0.8872 (p0) cc_final: 0.8458 (p0) REVERT: A 316 GLU cc_start: 0.8743 (tp30) cc_final: 0.8484 (tp30) REVERT: A 668 ARG cc_start: 0.8653 (ptt-90) cc_final: 0.8380 (ptt90) REVERT: A 694 ARG cc_start: 0.9162 (mmm-85) cc_final: 0.8907 (mmm-85) REVERT: B 46 ASN cc_start: 0.9167 (t0) cc_final: 0.8797 (t0) REVERT: B 81 CYS cc_start: 0.8915 (t) cc_final: 0.8083 (m) REVERT: B 110 ILE cc_start: 0.9366 (mm) cc_final: 0.9136 (mm) REVERT: B 141 ASP cc_start: 0.9165 (t0) cc_final: 0.8940 (p0) outliers start: 16 outliers final: 11 residues processed: 95 average time/residue: 0.0878 time to fit residues: 11.2892 Evaluate side-chains 86 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 585 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 53 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS ** A 540 ASN ** 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 = 0.3273 r_free = 0.3273 target = 0.077156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.057002 restraints weight = 19727.682| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 3.42 r_work: 0.2651 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7781 Z= 0.128 Angle : 0.554 10.634 10534 Z= 0.279 Chirality : 0.038 0.158 1144 Planarity : 0.004 0.042 1345 Dihedral : 5.790 108.583 1066 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.68 % Allowed : 28.21 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.02 (0.28), residues: 913 helix: 2.70 (0.21), residues: 610 sheet: 0.17 (1.43), residues: 11 loop : 0.60 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 668 TYR 0.014 0.001 TYR A 86 PHE 0.012 0.001 PHE A 569 TRP 0.009 0.001 TRP A 638 HIS 0.003 0.001 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 7781) covalent geometry : angle 0.55391 (10534) hydrogen bonds : bond 0.03277 ( 458) hydrogen bonds : angle 3.51147 ( 1326) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: A 108 MET cc_start: 0.9189 (tpp) cc_final: 0.8798 (tpp) REVERT: A 114 GLU cc_start: 0.9231 (tt0) cc_final: 0.8877 (tm-30) REVERT: A 133 ASP cc_start: 0.9439 (t70) cc_final: 0.9035 (t70) REVERT: A 200 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8306 (tm-30) REVERT: A 207 GLN cc_start: 0.9222 (OUTLIER) cc_final: 0.8813 (mp10) REVERT: A 220 ASP cc_start: 0.8888 (p0) cc_final: 0.8479 (p0) REVERT: A 316 GLU cc_start: 0.8751 (tp30) cc_final: 0.8503 (tp30) REVERT: A 668 ARG cc_start: 0.8645 (ptt-90) cc_final: 0.8403 (ptp90) REVERT: A 694 ARG cc_start: 0.9179 (mmm-85) cc_final: 0.8968 (mmm-85) REVERT: B 46 ASN cc_start: 0.9172 (t0) cc_final: 0.8804 (t0) REVERT: B 81 CYS cc_start: 0.8911 (t) cc_final: 0.8088 (m) REVERT: B 110 ILE cc_start: 0.9357 (mm) cc_final: 0.9136 (mm) REVERT: B 141 ASP cc_start: 0.9131 (t0) cc_final: 0.8871 (p0) outliers start: 14 outliers final: 11 residues processed: 85 average time/residue: 0.0975 time to fit residues: 10.8542 Evaluate side-chains 87 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain C residue 585 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 3.9990 chunk 20 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 41 optimal weight: 0.0170 chunk 44 optimal weight: 0.0470 chunk 82 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.2716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 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 = 0.3301 r_free = 0.3301 target = 0.078761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.058438 restraints weight = 19847.389| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 3.48 r_work: 0.2702 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7781 Z= 0.107 Angle : 0.540 10.181 10534 Z= 0.271 Chirality : 0.038 0.180 1144 Planarity : 0.004 0.042 1345 Dihedral : 5.593 102.880 1066 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.44 % Allowed : 28.69 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.10 (0.28), residues: 913 helix: 2.77 (0.21), residues: 604 sheet: 0.20 (1.46), residues: 11 loop : 0.70 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 668 TYR 0.010 0.001 TYR A 86 PHE 0.012 0.001 PHE A 569 TRP 0.009 0.001 TRP A 638 HIS 0.004 0.001 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 7781) covalent geometry : angle 0.53967 (10534) hydrogen bonds : bond 0.03039 ( 458) hydrogen bonds : angle 3.44874 ( 1326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1598.60 seconds wall clock time: 28 minutes 11.60 seconds (1691.60 seconds total)