Starting phenix.real_space_refine on Sat May 10 14:47:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k88_36947/05_2025/8k88_36947.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k88_36947/05_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_36947/05_2025/8k88_36947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k88_36947/05_2025/8k88_36947.map" model { file = "/net/cci-nas-00/data/ceres_data/8k88_36947/05_2025/8k88_36947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k88_36947/05_2025/8k88_36947.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.87, per 1000 atoms: 0.73 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: 2.11 Conformation dependent library (CDL) restraints added in 731.0 milliseconds 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: 2.54 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: 2.96 Time building geometry restraints manager: 2.46 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: 3.100 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 22.000 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:14.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.640 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP B 502 HIS 0.003 0.001 HIS A 11 PHE 0.008 0.001 PHE A 137 TYR 0.022 0.001 TYR A 341 ARG 0.010 0.001 ARG B 529 Details of bonding type rmsd hydrogen bonds : bond 0.14900 ( 297) hydrogen bonds : angle 6.07695 ( 811) covalent geometry : bond 0.00241 ( 6934) covalent geometry : angle 0.57789 ( 9594) *********************** 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 : 0.723 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: 1.4903 time to fit residues: 299.1654 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 : 0.717 ------------------------------------------------------------------------------- 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 63 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 0.0980 chunk 38 optimal weight: 9.9990 chunk 30 optimal weight: 0.0980 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 0.0470 chunk 68 optimal weight: 0.6980 overall best weight: 0.3478 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.120260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.108945 restraints weight = 9047.500| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.56 r_work: 0.3379 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6934 Z= 0.104 Angle : 0.524 7.630 9594 Z= 0.276 Chirality : 0.039 0.130 1074 Planarity : 0.005 0.052 1076 Dihedral : 18.364 170.167 1379 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.22 % Allowed : 23.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.33), residues: 722 helix: 2.42 (0.35), residues: 222 sheet: 0.96 (0.41), residues: 180 loop : 0.25 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 213 HIS 0.004 0.001 HIS B 437 PHE 0.015 0.001 PHE A 143 TYR 0.015 0.001 TYR A 366 ARG 0.007 0.001 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 297) hydrogen bonds : angle 4.29965 ( 811) covalent geometry : bond 0.00222 ( 6934) covalent geometry : angle 0.52422 ( 9594) *********************** 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 214 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 0.704 Fit side-chains REVERT: B 557 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8337 (p) outliers start: 20 outliers final: 8 residues processed: 199 average time/residue: 1.4110 time to fit residues: 292.2954 Evaluate side-chains 198 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 189 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 296 ASN Chi-restraints excluded: chain A residue 371 GLU 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 426 LEU Chi-restraints excluded: chain B residue 557 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 25 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.117365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.105947 restraints weight = 8978.803| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.56 r_work: 0.3334 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6934 Z= 0.156 Angle : 0.531 5.957 9594 Z= 0.279 Chirality : 0.040 0.141 1074 Planarity : 0.005 0.046 1076 Dihedral : 18.322 168.509 1371 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.05 % Allowed : 23.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.32), residues: 722 helix: 2.37 (0.35), residues: 222 sheet: 0.85 (0.41), residues: 180 loop : 0.19 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 502 HIS 0.004 0.001 HIS A 166 PHE 0.013 0.001 PHE A 304 TYR 0.015 0.001 TYR A 366 ARG 0.008 0.001 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 297) hydrogen bonds : angle 4.21522 ( 811) covalent geometry : bond 0.00357 ( 6934) covalent geometry : angle 0.53057 ( 9594) *********************** 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 205 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.543 Fit side-chains REVERT: B 358 GLU cc_start: 0.7952 (tp30) cc_final: 0.7745 (tp30) REVERT: B 504 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7499 (mmm) outliers start: 19 outliers final: 12 residues processed: 188 average time/residue: 1.4775 time to fit residues: 289.0384 Evaluate side-chains 196 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 183 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 303 ILE 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 426 LEU 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 8 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 58 optimal weight: 0.0040 chunk 74 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 22 optimal weight: 0.0980 chunk 60 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.119311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.107890 restraints weight = 9109.611| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.56 r_work: 0.3360 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6934 Z= 0.107 Angle : 0.503 5.884 9594 Z= 0.265 Chirality : 0.039 0.138 1074 Planarity : 0.004 0.041 1076 Dihedral : 18.148 165.710 1371 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.32), residues: 722 helix: 2.46 (0.35), residues: 222 sheet: 0.91 (0.41), residues: 180 loop : 0.20 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 502 HIS 0.002 0.000 HIS A 11 PHE 0.011 0.001 PHE A 304 TYR 0.014 0.001 TYR A 366 ARG 0.008 0.001 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.03242 ( 297) hydrogen bonds : angle 4.09122 ( 811) covalent geometry : bond 0.00237 ( 6934) covalent geometry : angle 0.50293 ( 9594) *********************** 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: 21 poor density : 191 time to evaluate : 0.719 Fit side-chains REVERT: B 504 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7532 (mmm) REVERT: B 557 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8322 (p) outliers start: 21 outliers final: 12 residues processed: 196 average time/residue: 1.4061 time to fit residues: 287.1355 Evaluate side-chains 199 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 294 SER 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 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 390 ILE Chi-restraints excluded: chain B residue 415 THR 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 29 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 19 optimal weight: 0.1980 chunk 15 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.117909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.106281 restraints weight = 9087.635| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.57 r_work: 0.3335 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1427 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= 0.136 Angle : 0.515 5.964 9594 Z= 0.271 Chirality : 0.040 0.144 1074 Planarity : 0.005 0.041 1076 Dihedral : 18.186 167.083 1371 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.05 % Allowed : 23.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.32), residues: 722 helix: 2.48 (0.35), residues: 222 sheet: 0.88 (0.41), residues: 180 loop : 0.16 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 502 HIS 0.003 0.001 HIS A 60 PHE 0.012 0.001 PHE A 304 TYR 0.015 0.001 TYR A 366 ARG 0.011 0.001 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 297) hydrogen bonds : angle 4.08717 ( 811) covalent geometry : bond 0.00309 ( 6934) covalent geometry : angle 0.51468 ( 9594) *********************** 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 210 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 0.711 Fit side-chains REVERT: B 504 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7546 (mmm) outliers start: 19 outliers final: 10 residues processed: 197 average time/residue: 1.3952 time to fit residues: 286.3171 Evaluate side-chains 200 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 294 SER 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 426 LEU Chi-restraints excluded: chain B residue 504 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 40 optimal weight: 0.0980 chunk 11 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 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 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.115714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.104104 restraints weight = 8992.388| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.55 r_work: 0.3304 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6934 Z= 0.201 Angle : 0.551 5.978 9594 Z= 0.289 Chirality : 0.042 0.156 1074 Planarity : 0.005 0.040 1076 Dihedral : 18.369 171.111 1371 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.22 % Allowed : 24.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.32), residues: 722 helix: 2.30 (0.35), residues: 222 sheet: 0.79 (0.41), residues: 180 loop : 0.08 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 502 HIS 0.004 0.001 HIS A 60 PHE 0.014 0.001 PHE A 304 TYR 0.016 0.001 TYR A 341 ARG 0.010 0.001 ARG B 529 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 297) hydrogen bonds : angle 4.24171 ( 811) covalent geometry : bond 0.00466 ( 6934) covalent geometry : angle 0.55105 ( 9594) *********************** 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 210 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 190 time to evaluate : 0.667 Fit side-chains REVERT: A 470 ARG cc_start: 0.8153 (mmt-90) cc_final: 0.7939 (mtp180) outliers start: 20 outliers final: 12 residues processed: 195 average time/residue: 1.4212 time to fit residues: 288.4485 Evaluate side-chains 196 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 184 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 197 MET 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 B residue 347 VAL Chi-restraints excluded: chain B residue 361 GLU 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 73 optimal weight: 0.0970 chunk 74 optimal weight: 2.9990 chunk 12 optimal weight: 0.0030 chunk 8 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.118500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.106867 restraints weight = 9105.135| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.57 r_work: 0.3348 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6934 Z= 0.116 Angle : 0.516 5.899 9594 Z= 0.273 Chirality : 0.039 0.141 1074 Planarity : 0.005 0.049 1076 Dihedral : 18.199 167.234 1371 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.05 % Allowed : 24.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.32), residues: 722 helix: 2.42 (0.35), residues: 222 sheet: 0.78 (0.41), residues: 180 loop : 0.11 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 502 HIS 0.002 0.001 HIS A 419 PHE 0.011 0.001 PHE A 304 TYR 0.015 0.001 TYR A 366 ARG 0.012 0.001 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.03234 ( 297) hydrogen bonds : angle 4.10702 ( 811) covalent geometry : bond 0.00260 ( 6934) covalent geometry : angle 0.51643 ( 9594) *********************** 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 216 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.681 Fit side-chains REVERT: A 144 ASP cc_start: 0.8300 (m-30) cc_final: 0.8018 (m-30) REVERT: A 450 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7883 (tm-30) REVERT: B 566 GLU cc_start: 0.7835 (tp30) cc_final: 0.7595 (tp30) outliers start: 19 outliers final: 13 residues processed: 202 average time/residue: 1.3744 time to fit residues: 289.3044 Evaluate side-chains 205 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 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 303 ILE 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 17 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 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 = 0.3584 r_free = 0.3584 target = 0.116613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.104969 restraints weight = 9044.882| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.56 r_work: 0.3315 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6934 Z= 0.175 Angle : 0.539 5.931 9594 Z= 0.283 Chirality : 0.041 0.148 1074 Planarity : 0.005 0.043 1076 Dihedral : 18.337 169.999 1371 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.73 % Allowed : 26.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.32), residues: 722 helix: 2.35 (0.35), residues: 222 sheet: 0.64 (0.42), residues: 174 loop : 0.08 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 502 HIS 0.003 0.001 HIS A 60 PHE 0.020 0.001 PHE B 579 TYR 0.014 0.001 TYR A 341 ARG 0.010 0.001 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 297) hydrogen bonds : angle 4.20987 ( 811) covalent geometry : bond 0.00406 ( 6934) covalent geometry : angle 0.53912 ( 9594) *********************** 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 209 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 0.722 Fit side-chains REVERT: A 470 ARG cc_start: 0.8129 (mmt-90) cc_final: 0.7924 (mtp180) REVERT: B 326 LYS cc_start: 0.5932 (pttm) cc_final: 0.5477 (pttm) REVERT: B 557 VAL cc_start: 0.8536 (OUTLIER) cc_final: 0.8322 (p) REVERT: B 566 GLU cc_start: 0.7824 (tp30) cc_final: 0.7570 (tp30) outliers start: 17 outliers final: 13 residues processed: 196 average time/residue: 1.3779 time to fit residues: 281.3389 Evaluate side-chains 194 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 197 MET 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 B residue 347 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 557 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 52 optimal weight: 0.1980 chunk 32 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.117522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.105798 restraints weight = 9187.748| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.57 r_work: 0.3325 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6934 Z= 0.142 Angle : 0.527 6.081 9594 Z= 0.278 Chirality : 0.040 0.143 1074 Planarity : 0.005 0.041 1076 Dihedral : 18.242 168.994 1371 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.73 % Allowed : 26.05 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.32), residues: 722 helix: 2.35 (0.35), residues: 222 sheet: 0.64 (0.42), residues: 174 loop : 0.10 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 502 HIS 0.002 0.001 HIS A 166 PHE 0.015 0.001 PHE B 579 TYR 0.013 0.001 TYR A 366 ARG 0.010 0.001 ARG B 529 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 297) hydrogen bonds : angle 4.15255 ( 811) covalent geometry : bond 0.00328 ( 6934) covalent geometry : angle 0.52728 ( 9594) *********************** 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: 17 poor density : 185 time to evaluate : 0.715 Fit side-chains REVERT: A 144 ASP cc_start: 0.8302 (m-30) cc_final: 0.8015 (m-30) REVERT: B 326 LYS cc_start: 0.5871 (pttm) cc_final: 0.5284 (pttm) REVERT: B 566 GLU cc_start: 0.7824 (tp30) cc_final: 0.7553 (tp30) outliers start: 17 outliers final: 13 residues processed: 191 average time/residue: 1.5707 time to fit residues: 312.3168 Evaluate side-chains 200 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 187 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 197 MET 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 B residue 347 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 399 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 42 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 58 optimal weight: 0.0470 chunk 18 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.0470 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.118247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.106406 restraints weight = 9159.588| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.61 r_work: 0.3335 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6934 Z= 0.119 Angle : 0.528 6.467 9594 Z= 0.278 Chirality : 0.040 0.140 1074 Planarity : 0.005 0.043 1076 Dihedral : 18.244 168.639 1371 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.93 % Allowed : 26.69 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.32), residues: 722 helix: 2.38 (0.35), residues: 222 sheet: 0.65 (0.41), residues: 177 loop : 0.11 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 502 HIS 0.002 0.001 HIS A 166 PHE 0.016 0.001 PHE B 579 TYR 0.012 0.001 TYR A 366 ARG 0.010 0.001 ARG B 529 Details of bonding type rmsd hydrogen bonds : bond 0.03317 ( 297) hydrogen bonds : angle 4.14876 ( 811) covalent geometry : bond 0.00269 ( 6934) covalent geometry : angle 0.52786 ( 9594) ********************** 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 201 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 189 time to evaluate : 0.578 Fit side-chains REVERT: A 144 ASP cc_start: 0.8298 (m-30) cc_final: 0.8017 (m-30) REVERT: A 317 GLN cc_start: 0.8427 (mm-40) cc_final: 0.8154 (mm-40) REVERT: B 326 LYS cc_start: 0.5810 (pttm) cc_final: 0.5202 (pttm) REVERT: B 566 GLU cc_start: 0.7838 (tp30) cc_final: 0.7567 (tp30) outliers start: 12 outliers final: 11 residues processed: 191 average time/residue: 1.4468 time to fit residues: 288.0213 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 : 0.701 ------------------------------------------------------------------------------- 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 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 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 390 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 3 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 19 optimal weight: 0.0370 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 overall best weight: 0.8660 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.117901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.106170 restraints weight = 9098.999| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.58 r_work: 0.3333 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6934 Z= 0.137 Angle : 0.528 6.456 9594 Z= 0.277 Chirality : 0.040 0.146 1074 Planarity : 0.005 0.042 1076 Dihedral : 18.226 168.568 1371 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.25 % Allowed : 27.01 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.32), residues: 722 helix: 2.39 (0.35), residues: 222 sheet: 0.64 (0.42), residues: 174 loop : 0.11 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 502 HIS 0.002 0.001 HIS A 166 PHE 0.016 0.001 PHE B 579 TYR 0.012 0.001 TYR A 366 ARG 0.010 0.001 ARG B 529 Details of bonding type rmsd hydrogen bonds : bond 0.03375 ( 297) hydrogen bonds : angle 4.14430 ( 811) covalent geometry : bond 0.00316 ( 6934) covalent geometry : angle 0.52801 ( 9594) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6944.48 seconds wall clock time: 120 minutes 22.68 seconds (7222.68 seconds total)