Starting phenix.real_space_refine on Fri Aug 22 17:28:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k88_36947/08_2025/8k88_36947.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k88_36947/08_2025/8k88_36947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k88_36947/08_2025/8k88_36947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k88_36947/08_2025/8k88_36947.map" model { file = "/net/cci-nas-00/data/ceres_data/8k88_36947/08_2025/8k88_36947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k88_36947/08_2025/8k88_36947.cif" } resolution = 2.6 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= 0.005 sd= 0.050 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 P 44 5.49 5 Mg 1 5.21 5 S 22 5.16 5 C 4124 2.51 5 N 1150 2.21 5 O 1345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6686 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 469 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 444 Classifications: {'DNA': 1, 'RNA': 20} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 7, 'rna3p_pyr': 9} Link IDs: {'rna2p': 4, 'rna3p': 16} Chain: "A" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3719 Classifications: {'peptide': 468} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 439} Chain: "B" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2053 Classifications: {'peptide': 258} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 247} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.71, per 1000 atoms: 0.26 Number of scatterers: 6686 At special positions: 0 Unit cell: (74.6512, 90.2876, 107.437, 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) S 22 16.00 P 44 15.00 Mg 1 11.99 O 1345 8.00 N 1150 7.00 C 4124 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: 0.49 Conformation dependent library (CDL) restraints added in 307.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 38.7% alpha, 24.1% beta 18 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 22 through 24 No H-bonds generated for 'chain 'A' and resid 22 through 24' Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 39 through 45 removed outlier: 3.883A pdb=" N CYS A 43 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 60 through 72 removed outlier: 3.735A pdb=" N LEU A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 95 Processing helix chain 'A' and resid 111 through 120 removed outlier: 3.949A pdb=" N GLY A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'A' and resid 134 through 138 removed outlier: 3.705A pdb=" N ARG A 138 " --> pdb=" O GLY A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 151 through 158 removed outlier: 4.920A pdb=" N LYS A 156 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 184 through 189 removed outlier: 3.891A pdb=" N LEU A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 209 removed outlier: 3.680A pdb=" N VAL A 196 " --> pdb=" O CYS A 192 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY A 209 " --> pdb=" O TYR A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 295 Processing helix chain 'A' and resid 312 through 323 removed outlier: 3.634A pdb=" N PHE A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 429 removed outlier: 4.266A pdb=" N THR A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 459 Processing helix chain 'A' and resid 460 through 463 removed outlier: 4.024A pdb=" N VAL A 463 " --> pdb=" O PRO A 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 460 through 463' Processing helix chain 'A' and resid 470 through 472 No H-bonds generated for 'chain 'A' and resid 470 through 472' Processing helix chain 'B' and resid 355 through 367 Processing helix chain 'B' and resid 383 through 391 removed outlier: 3.601A pdb=" N ILE B 387 " --> pdb=" O GLY B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 414 Processing helix chain 'B' and resid 414 through 430 Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 458 through 465 Processing helix chain 'B' and resid 513 through 519 removed outlier: 4.968A pdb=" N GLU B 518 " --> pdb=" O ASP B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 529 Processing helix chain 'B' and resid 532 through 549 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 6.156A pdb=" N LEU A 331 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA A 223 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N HIS A 306 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE A 225 " --> pdb=" O HIS A 306 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 removed outlier: 8.324A pdb=" N CYS A 107 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TYR A 54 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 99 removed outlier: 6.190A pdb=" N ARG A 51 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU A 147 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA A 53 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N TYR A 149 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU A 55 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU A 146 " --> pdb=" O GLN A 181 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ILE A 183 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL A 148 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA6, first strand: chain 'A' and resid 355 through 356 removed outlier: 3.624A pdb=" N ALA A 355 " --> pdb=" O ASP A 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 381 through 382 Processing sheet with id=AA8, first strand: chain 'B' and resid 335 through 337 removed outlier: 4.262A pdb=" N HIS B 444 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 335 through 337 Processing sheet with id=AB1, first strand: chain 'B' and resid 370 through 374 removed outlier: 3.739A pdb=" N VAL B 378 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLY B 382 " --> pdb=" O ARG B 344 " (cutoff:3.500A) removed outlier: 11.045A pdb=" N ARG B 344 " --> pdb=" O GLY B 382 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE B 343 " --> pdb=" O TYR B 403 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TYR B 403 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N CYS B 345 " --> pdb=" O GLN B 401 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLN B 401 " --> pdb=" O CYS B 345 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL B 347 " --> pdb=" O ILE B 399 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE B 399 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N THR B 349 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 556 through 561 271 hydrogen bonds defined for protein. 723 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1887 1.34 - 1.45: 1374 1.45 - 1.57: 3555 1.57 - 1.69: 86 1.69 - 1.81: 32 Bond restraints: 6934 Sorted by residual: bond pdb=" CB GLU B 566 " pdb=" CG GLU B 566 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" N THR A 242 " pdb=" CA THR A 242 " ideal model delta sigma weight residual 1.457 1.472 -0.014 1.29e-02 6.01e+03 1.22e+00 bond pdb=" CB GLU B 496 " pdb=" CG GLU B 496 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.19e+00 bond pdb=" C3' DA C 15 " pdb=" C2' DA C 15 " ideal model delta sigma weight residual 1.525 1.545 -0.020 2.00e-02 2.50e+03 1.01e+00 bond pdb=" C3' DT C 13 " pdb=" O3' DT C 13 " ideal model delta sigma weight residual 1.422 1.452 -0.030 3.00e-02 1.11e+03 1.00e+00 ... (remaining 6929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 9399 1.78 - 3.55: 168 3.55 - 5.33: 19 5.33 - 7.10: 6 7.10 - 8.88: 2 Bond angle restraints: 9594 Sorted by residual: angle pdb=" C SER B 327 " pdb=" N PHE B 328 " pdb=" CA PHE B 328 " ideal model delta sigma weight residual 121.48 127.26 -5.78 2.04e+00 2.40e-01 8.02e+00 angle pdb=" CA GLU B 496 " pdb=" CB GLU B 496 " pdb=" CG GLU B 496 " ideal model delta sigma weight residual 114.10 119.28 -5.18 2.00e+00 2.50e-01 6.71e+00 angle pdb=" CA LEU A 146 " pdb=" CB LEU A 146 " pdb=" CG LEU A 146 " ideal model delta sigma weight residual 116.30 125.18 -8.88 3.50e+00 8.16e-02 6.43e+00 angle pdb=" CB GLU B 566 " pdb=" CG GLU B 566 " pdb=" CD GLU B 566 " ideal model delta sigma weight residual 112.60 116.90 -4.30 1.70e+00 3.46e-01 6.38e+00 angle pdb=" CB MET B 504 " pdb=" CG MET B 504 " pdb=" SD MET B 504 " ideal model delta sigma weight residual 112.70 120.22 -7.52 3.00e+00 1.11e-01 6.29e+00 ... (remaining 9589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.39: 3828 34.39 - 68.77: 273 68.77 - 103.16: 14 103.16 - 137.54: 1 137.54 - 171.93: 1 Dihedral angle restraints: 4117 sinusoidal: 2007 harmonic: 2110 Sorted by residual: dihedral pdb=" O4' U D 2 " pdb=" C1' U D 2 " pdb=" N1 U D 2 " pdb=" C2 U D 2 " ideal model delta sinusoidal sigma weight residual -160.00 11.93 -171.93 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" CG ARG A 69 " pdb=" CD ARG A 69 " pdb=" NE ARG A 69 " pdb=" CZ ARG A 69 " ideal model delta sinusoidal sigma weight residual -90.00 -37.10 -52.90 2 1.50e+01 4.44e-03 1.36e+01 dihedral pdb=" C4' DT C 13 " pdb=" C3' DT C 13 " pdb=" O3' DT C 13 " pdb=" P DA C 14 " ideal model delta sinusoidal sigma weight residual 220.00 103.43 116.57 1 3.50e+01 8.16e-04 1.13e+01 ... (remaining 4114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 708 0.029 - 0.059: 250 0.059 - 0.088: 55 0.088 - 0.117: 56 0.117 - 0.146: 5 Chirality restraints: 1074 Sorted by residual: chirality pdb=" C1' G D 15 " pdb=" O4' G D 15 " pdb=" C2' G D 15 " pdb=" N9 G D 15 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" C1' A D 4 " pdb=" O4' A D 4 " pdb=" C2' A D 4 " pdb=" N9 A D 4 " both_signs ideal model delta sigma weight residual False 2.46 2.33 0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA THR A 242 " pdb=" N THR A 242 " pdb=" C THR A 242 " pdb=" CB THR A 242 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.12 2.00e-01 2.50e+01 3.85e-01 ... (remaining 1071 not shown) Planarity restraints: 1076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 389 " 0.042 5.00e-02 4.00e+02 6.47e-02 6.71e+00 pdb=" N PRO A 390 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 390 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 390 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A D 4 " -0.029 2.00e-02 2.50e+03 1.30e-02 4.68e+00 pdb=" N9 A D 4 " 0.030 2.00e-02 2.50e+03 pdb=" C8 A D 4 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A D 4 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A D 4 " 0.004 2.00e-02 2.50e+03 pdb=" C6 A D 4 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A D 4 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A D 4 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A D 4 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A D 4 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A D 4 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 401 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO A 402 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 402 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 402 " -0.029 5.00e-02 4.00e+02 ... (remaining 1073 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 44 2.56 - 3.14: 4837 3.14 - 3.73: 10670 3.73 - 4.31: 15184 4.31 - 4.90: 24623 Nonbonded interactions: 55358 Sorted by model distance: nonbonded pdb=" OXT MET A 473 " pdb="MG MG A 501 " model vdw 1.973 2.170 nonbonded pdb=" OP1 A D 3 " pdb="MG MG A 501 " model vdw 1.987 2.170 nonbonded pdb=" OP2 A D 1 " pdb="MG MG A 501 " model vdw 2.070 2.170 nonbonded pdb=" O THR A 242 " pdb=" OG1 THR A 262 " model vdw 2.206 3.040 nonbonded pdb=" OD1 ASN A 195 " pdb=" ND2 ASN A 436 " model vdw 2.212 3.120 ... (remaining 55353 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: 1.700 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: 0.230 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.360 Find NCS groups from input model: 0.020 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:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 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 : 0.002 0.034 6934 Z= 0.123 Angle : 0.578 8.877 9594 Z= 0.310 Chirality : 0.038 0.146 1074 Planarity : 0.005 0.065 1076 Dihedral : 20.288 171.926 2761 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.96 % Allowed : 27.97 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.32), residues: 722 helix: 2.27 (0.35), residues: 221 sheet: 0.96 (0.40), residues: 180 loop : 0.16 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 529 TYR 0.022 0.001 TYR A 341 PHE 0.008 0.001 PHE A 137 TRP 0.006 0.001 TRP B 502 HIS 0.003 0.001 HIS A 11 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 6934) covalent geometry : angle 0.57789 ( 9594) hydrogen bonds : bond 0.14900 ( 297) hydrogen bonds : angle 6.07695 ( 811) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 191 time to evaluate : 0.178 Fit side-chains REVERT: A 156 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8197 (ptmm) outliers start: 6 outliers final: 3 residues processed: 193 average time/residue: 0.6861 time to fit residues: 137.7084 Evaluate side-chains 188 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 184 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 463 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 GLN A 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.117484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.106100 restraints weight = 9133.901| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.57 r_work: 0.3336 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6934 Z= 0.146 Angle : 0.542 7.747 9594 Z= 0.285 Chirality : 0.040 0.140 1074 Planarity : 0.005 0.054 1076 Dihedral : 18.412 171.665 1379 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.22 % Allowed : 23.79 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.32), residues: 722 helix: 2.33 (0.35), residues: 222 sheet: 0.88 (0.40), residues: 180 loop : 0.22 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 69 TYR 0.016 0.001 TYR A 366 PHE 0.016 0.001 PHE A 143 TRP 0.007 0.001 TRP B 502 HIS 0.004 0.001 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6934) covalent geometry : angle 0.54187 ( 9594) hydrogen bonds : bond 0.03876 ( 297) hydrogen bonds : angle 4.35437 ( 811) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 0.244 Fit side-chains outliers start: 20 outliers final: 12 residues processed: 191 average time/residue: 0.6478 time to fit residues: 128.6072 Evaluate side-chains 197 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 185 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 0.0470 chunk 30 optimal weight: 5.9990 chunk 72 optimal weight: 0.0870 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS A 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.118496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.107011 restraints weight = 8981.786| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.57 r_work: 0.3351 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6934 Z= 0.120 Angle : 0.519 5.955 9594 Z= 0.273 Chirality : 0.039 0.138 1074 Planarity : 0.005 0.046 1076 Dihedral : 18.313 168.121 1371 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.05 % Allowed : 23.31 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.32), residues: 722 helix: 2.36 (0.35), residues: 222 sheet: 0.92 (0.41), residues: 180 loop : 0.17 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 62 TYR 0.013 0.001 TYR A 366 PHE 0.012 0.001 PHE A 304 TRP 0.008 0.001 TRP B 502 HIS 0.003 0.001 HIS A 11 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 6934) covalent geometry : angle 0.51860 ( 9594) hydrogen bonds : bond 0.03503 ( 297) hydrogen bonds : angle 4.18267 ( 811) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.157 Fit side-chains REVERT: A 14 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8514 (mm) REVERT: A 408 MET cc_start: 0.8447 (ttp) cc_final: 0.8138 (ttm) REVERT: B 358 GLU cc_start: 0.7925 (tp30) cc_final: 0.7719 (tp30) REVERT: B 504 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7542 (mmm) outliers start: 19 outliers final: 9 residues processed: 187 average time/residue: 0.6107 time to fit residues: 118.7428 Evaluate side-chains 198 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 187 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 504 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 20 optimal weight: 0.4980 chunk 27 optimal weight: 0.4980 chunk 67 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 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 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.118544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.107177 restraints weight = 9030.531| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.56 r_work: 0.3345 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6934 Z= 0.123 Angle : 0.506 5.938 9594 Z= 0.267 Chirality : 0.039 0.140 1074 Planarity : 0.004 0.042 1076 Dihedral : 18.206 167.419 1371 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.70 % Allowed : 22.99 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.33), residues: 722 helix: 2.44 (0.35), residues: 222 sheet: 0.90 (0.41), residues: 180 loop : 0.16 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 69 TYR 0.014 0.001 TYR A 366 PHE 0.012 0.001 PHE A 304 TRP 0.008 0.001 TRP B 502 HIS 0.002 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6934) covalent geometry : angle 0.50598 ( 9594) hydrogen bonds : bond 0.03374 ( 297) hydrogen bonds : angle 4.10618 ( 811) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.177 Fit side-chains REVERT: B 504 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.7527 (mmm) REVERT: B 557 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8323 (p) outliers start: 23 outliers final: 10 residues processed: 196 average time/residue: 0.5896 time to fit residues: 120.3099 Evaluate side-chains 190 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 557 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 2 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 29 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 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.116551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.104925 restraints weight = 9168.887| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.56 r_work: 0.3317 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6934 Z= 0.175 Angle : 0.533 5.983 9594 Z= 0.281 Chirality : 0.041 0.150 1074 Planarity : 0.005 0.040 1076 Dihedral : 18.291 170.247 1371 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.38 % Allowed : 23.31 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.32), residues: 722 helix: 2.34 (0.35), residues: 222 sheet: 0.82 (0.41), residues: 180 loop : 0.10 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 62 TYR 0.016 0.001 TYR A 366 PHE 0.014 0.001 PHE A 304 TRP 0.009 0.001 TRP B 502 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 6934) covalent geometry : angle 0.53263 ( 9594) hydrogen bonds : bond 0.03711 ( 297) hydrogen bonds : angle 4.18543 ( 811) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.248 Fit side-chains REVERT: A 49 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8408 (pt0) outliers start: 21 outliers final: 13 residues processed: 191 average time/residue: 0.6476 time to fit residues: 128.7037 Evaluate side-chains 193 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 59 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 58 optimal weight: 0.0770 chunk 63 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.118209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.106537 restraints weight = 9216.734| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.58 r_work: 0.3341 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6934 Z= 0.117 Angle : 0.511 5.924 9594 Z= 0.270 Chirality : 0.039 0.142 1074 Planarity : 0.004 0.039 1076 Dihedral : 18.212 168.286 1371 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.54 % Allowed : 24.12 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.32), residues: 722 helix: 2.39 (0.35), residues: 222 sheet: 0.85 (0.41), residues: 180 loop : 0.13 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 69 TYR 0.013 0.001 TYR A 366 PHE 0.011 0.001 PHE A 304 TRP 0.008 0.001 TRP B 502 HIS 0.002 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 6934) covalent geometry : angle 0.51129 ( 9594) hydrogen bonds : bond 0.03314 ( 297) hydrogen bonds : angle 4.09952 ( 811) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.210 Fit side-chains REVERT: A 49 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8359 (pt0) outliers start: 22 outliers final: 12 residues processed: 191 average time/residue: 0.6619 time to fit residues: 131.6523 Evaluate side-chains 195 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 9 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN A 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.117942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.106327 restraints weight = 9112.780| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.56 r_work: 0.3337 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6934 Z= 0.130 Angle : 0.515 5.933 9594 Z= 0.271 Chirality : 0.039 0.144 1074 Planarity : 0.005 0.042 1076 Dihedral : 18.228 168.286 1371 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.89 % Allowed : 24.60 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.33), residues: 722 helix: 2.38 (0.35), residues: 222 sheet: 0.82 (0.41), residues: 180 loop : 0.14 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 529 TYR 0.015 0.001 TYR A 366 PHE 0.011 0.001 PHE A 304 TRP 0.008 0.001 TRP B 502 HIS 0.002 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6934) covalent geometry : angle 0.51500 ( 9594) hydrogen bonds : bond 0.03332 ( 297) hydrogen bonds : angle 4.09165 ( 811) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.222 Fit side-chains outliers start: 18 outliers final: 15 residues processed: 192 average time/residue: 0.6831 time to fit residues: 136.7561 Evaluate side-chains 197 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 72 optimal weight: 0.0040 chunk 16 optimal weight: 2.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN A 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.117002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.105412 restraints weight = 9040.244| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.56 r_work: 0.3323 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6934 Z= 0.162 Angle : 0.534 5.926 9594 Z= 0.280 Chirality : 0.040 0.151 1074 Planarity : 0.005 0.051 1076 Dihedral : 18.286 169.990 1371 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.22 % Allowed : 24.92 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.32), residues: 722 helix: 2.33 (0.35), residues: 222 sheet: 0.65 (0.41), residues: 174 loop : 0.10 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 62 TYR 0.015 0.001 TYR A 366 PHE 0.016 0.001 PHE A 257 TRP 0.009 0.001 TRP B 502 HIS 0.003 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 6934) covalent geometry : angle 0.53383 ( 9594) hydrogen bonds : bond 0.03545 ( 297) hydrogen bonds : angle 4.14473 ( 811) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.180 Fit side-chains REVERT: A 450 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7889 (tm-30) REVERT: B 459 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8536 (mp) REVERT: B 504 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7397 (mmm) outliers start: 20 outliers final: 15 residues processed: 190 average time/residue: 0.6866 time to fit residues: 135.7059 Evaluate side-chains 201 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 504 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 40 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 67 optimal weight: 0.0070 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN A 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.117636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.106051 restraints weight = 9132.089| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.57 r_work: 0.3331 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6934 Z= 0.127 Angle : 0.529 6.012 9594 Z= 0.278 Chirality : 0.040 0.146 1074 Planarity : 0.005 0.051 1076 Dihedral : 18.273 169.486 1371 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.05 % Allowed : 24.76 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.32), residues: 722 helix: 2.35 (0.35), residues: 222 sheet: 0.63 (0.42), residues: 174 loop : 0.10 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 62 TYR 0.014 0.001 TYR A 366 PHE 0.013 0.001 PHE A 257 TRP 0.008 0.001 TRP B 502 HIS 0.003 0.001 HIS A 419 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6934) covalent geometry : angle 0.52898 ( 9594) hydrogen bonds : bond 0.03390 ( 297) hydrogen bonds : angle 4.13006 ( 811) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.232 Fit side-chains REVERT: A 450 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: B 459 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8532 (mp) REVERT: B 504 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7472 (mmm) outliers start: 19 outliers final: 15 residues processed: 186 average time/residue: 0.7366 time to fit residues: 142.6456 Evaluate side-chains 201 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 504 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 28 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 0.0170 chunk 49 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 21 optimal weight: 0.1980 chunk 11 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 HIS A 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.118822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.107274 restraints weight = 9134.423| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.56 r_work: 0.3352 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 6934 Z= 0.111 Angle : 0.523 6.689 9594 Z= 0.275 Chirality : 0.039 0.141 1074 Planarity : 0.005 0.048 1076 Dihedral : 18.217 168.020 1371 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.57 % Allowed : 24.76 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.33), residues: 722 helix: 2.36 (0.35), residues: 222 sheet: 0.62 (0.42), residues: 174 loop : 0.14 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 62 TYR 0.014 0.001 TYR A 366 PHE 0.011 0.001 PHE A 257 TRP 0.008 0.001 TRP B 502 HIS 0.002 0.000 HIS A 419 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6934) covalent geometry : angle 0.52349 ( 9594) hydrogen bonds : bond 0.03226 ( 297) hydrogen bonds : angle 4.10186 ( 811) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.247 Fit side-chains REVERT: B 459 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8532 (mp) REVERT: B 504 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7470 (mmm) outliers start: 16 outliers final: 13 residues processed: 189 average time/residue: 0.7610 time to fit residues: 149.7888 Evaluate side-chains 198 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 504 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 68 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 60 optimal weight: 0.0970 chunk 62 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.116754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.105073 restraints weight = 9049.090| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.57 r_work: 0.3313 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6934 Z= 0.175 Angle : 0.547 6.532 9594 Z= 0.286 Chirality : 0.041 0.153 1074 Planarity : 0.005 0.045 1076 Dihedral : 18.322 171.056 1371 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.77 % Allowed : 26.21 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.32), residues: 722 helix: 2.27 (0.35), residues: 222 sheet: 0.62 (0.41), residues: 177 loop : 0.07 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 62 TYR 0.014 0.001 TYR A 341 PHE 0.024 0.001 PHE B 579 TRP 0.009 0.001 TRP B 502 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 6934) covalent geometry : angle 0.54685 ( 9594) hydrogen bonds : bond 0.03613 ( 297) hydrogen bonds : angle 4.16776 ( 811) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3294.24 seconds wall clock time: 56 minutes 47.33 seconds (3407.33 seconds total)