Starting phenix.real_space_refine on Tue Aug 4 17:39:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrq_37786/08_2026/8wrq_37786.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrq_37786/08_2026/8wrq_37786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wrq_37786/08_2026/8wrq_37786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrq_37786/08_2026/8wrq_37786.map" model { file = "/net/cci-nas-00/data/ceres_data/8wrq_37786/08_2026/8wrq_37786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrq_37786/08_2026/8wrq_37786.cif" } resolution = 3.05 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= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 60 5.49 5 S 9 5.16 5 C 3367 2.51 5 N 1023 2.21 5 O 1176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5635 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4386 Classifications: {'peptide': 549} Link IDs: {'PTRANS': 36, 'TRANS': 512} Chain breaks: 2 Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 627 Classifications: {'RNA': 30} Modifications used: {'rna2p_pyr': 8, 'rna3p_pur': 10, 'rna3p_pyr': 12} Link IDs: {'rna2p': 8, 'rna3p': 21} Chain: "C" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 419 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 203 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Time building chain proxies: 1.11, per 1000 atoms: 0.20 Number of scatterers: 5635 At special positions: 0 Unit cell: (89.1, 89.1, 124.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 P 60 15.00 O 1176 8.00 N 1023 7.00 C 3367 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: 0.46 Conformation dependent library (CDL) restraints added in 230.4 milliseconds 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1024 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 3 sheets defined 49.7% alpha, 11.1% beta 12 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.865A pdb=" N GLY A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 99 Processing helix chain 'A' and resid 105 through 117 removed outlier: 3.523A pdb=" N ARG A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 141 removed outlier: 3.991A pdb=" N LEU A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 156 removed outlier: 3.776A pdb=" N ARG A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.787A pdb=" N ILE A 238 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 309 through 319 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 369 through 381 removed outlier: 4.208A pdb=" N LEU A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 437 removed outlier: 3.546A pdb=" N ARG A 434 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A 435 " --> pdb=" O ARG A 431 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 449 removed outlier: 3.994A pdb=" N GLN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 465 removed outlier: 3.596A pdb=" N GLU A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 478 Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 493 through 502 removed outlier: 3.714A pdb=" N ASP A 497 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS A 502 " --> pdb=" O HIS A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 536 Processing helix chain 'A' and resid 546 through 556 removed outlier: 3.886A pdb=" N THR A 551 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TRP A 552 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG A 556 " --> pdb=" O TRP A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 588 removed outlier: 4.121A pdb=" N VAL A 562 " --> pdb=" O SER A 558 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG A 566 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 Processing helix chain 'A' and resid 637 through 642 Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.642A pdb=" N ASP A 342 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE A 347 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASN A 64 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL A 306 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN A 68 " --> pdb=" O TRP A 304 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TRP A 304 " --> pdb=" O GLN A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 411 through 420 removed outlier: 5.795A pdb=" N ALA A 413 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LYS A 405 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG A 403 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLY A 417 " --> pdb=" O PHE A 401 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 398 " --> pdb=" O ASP A 390 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 402 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY A 385 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL A 595 " --> pdb=" O GLY A 385 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL A 387 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLU A 597 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N ILE A 389 " --> pdb=" O GLU A 597 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 510 through 511 186 hydrogen bonds defined for protein. 513 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 0.75 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1382 1.33 - 1.45: 1356 1.45 - 1.57: 3012 1.57 - 1.69: 117 1.69 - 1.81: 13 Bond restraints: 5880 Sorted by residual: bond pdb=" C3' DT C -7 " pdb=" C2' DT C -7 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C1' DC C 7 " pdb=" N1 DC C 7 " ideal model delta sigma weight residual 1.468 1.504 -0.036 1.40e-02 5.10e+03 6.70e+00 bond pdb=" C1' DC D 0 " pdb=" N1 DC D 0 " ideal model delta sigma weight residual 1.468 1.504 -0.036 1.40e-02 5.10e+03 6.61e+00 bond pdb=" C3' DT C 3 " pdb=" C2' DT C 3 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.92e+00 bond pdb=" C3' DC D -6 " pdb=" C2' DC D -6 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.66e+00 ... (remaining 5875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 7913 1.71 - 3.42: 283 3.42 - 5.14: 21 5.14 - 6.85: 2 6.85 - 8.56: 1 Bond angle restraints: 8220 Sorted by residual: angle pdb=" O5' C B -19 " pdb=" C5' C B -19 " pdb=" C4' C B -19 " ideal model delta sigma weight residual 109.40 113.09 -3.69 8.00e-01 1.56e+00 2.13e+01 angle pdb=" N3 DT C 3 " pdb=" C4 DT C 3 " pdb=" O4 DT C 3 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT D -2 " pdb=" C4 DT D -2 " pdb=" O4 DT D -2 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT C -7 " pdb=" C4 DT C -7 " pdb=" O4 DT C -7 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT D -1 " pdb=" C4 DT D -1 " pdb=" O4 DT D -1 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 ... (remaining 8215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 3328 35.89 - 71.79: 207 71.79 - 107.68: 17 107.68 - 143.57: 0 143.57 - 179.47: 3 Dihedral angle restraints: 3555 sinusoidal: 1971 harmonic: 1584 Sorted by residual: dihedral pdb=" O4' C B 8 " pdb=" C1' C B 8 " pdb=" N1 C B 8 " pdb=" C2 C B 8 " ideal model delta sinusoidal sigma weight residual -128.00 51.47 -179.47 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B -9 " pdb=" C1' U B -9 " pdb=" N1 U B -9 " pdb=" C2 U B -9 " ideal model delta sinusoidal sigma weight residual -128.00 47.46 -175.46 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" C4' DG D -8 " pdb=" C3' DG D -8 " pdb=" O3' DG D -8 " pdb=" P DG D -7 " ideal model delta sinusoidal sigma weight residual -140.00 31.87 -171.87 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 3552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 627 0.040 - 0.079: 205 0.079 - 0.119: 71 0.119 - 0.159: 30 0.159 - 0.198: 1 Chirality restraints: 934 Sorted by residual: chirality pdb=" C3' DG D -8 " pdb=" C4' DG D -8 " pdb=" O3' DG D -8 " pdb=" C2' DG D -8 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.84e-01 chirality pdb=" CB VAL A 524 " pdb=" CA VAL A 524 " pdb=" CG1 VAL A 524 " pdb=" CG2 VAL A 524 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" C2' G B -11 " pdb=" C3' G B -11 " pdb=" O2' G B -11 " pdb=" C1' G B -11 " both_signs ideal model delta sigma weight residual False -2.62 -2.75 0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 931 not shown) Planarity restraints: 836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 118 " 0.073 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO A 119 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO A 119 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 119 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 414 " 0.072 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO A 415 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 273 " -0.043 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO A 274 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 274 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 274 " -0.036 5.00e-02 4.00e+02 ... (remaining 833 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 779 2.76 - 3.29: 5112 3.29 - 3.83: 9609 3.83 - 4.36: 11476 4.36 - 4.90: 18115 Nonbonded interactions: 45091 Sorted by model distance: nonbonded pdb=" NZ LYS A 633 " pdb=" OD2 ASP A 637 " model vdw 2.221 3.120 nonbonded pdb=" ND2 ASN A 138 " pdb=" OP1 DG C -2 " model vdw 2.294 3.120 nonbonded pdb=" O LYS A 145 " pdb=" OG1 THR A 149 " model vdw 2.302 3.040 nonbonded pdb=" O SER A 466 " pdb=" NH1 ARG A 536 " model vdw 2.317 3.120 nonbonded pdb=" NH1 ARG A 106 " pdb=" OP1 DA D -3 " model vdw 2.334 3.120 ... (remaining 45086 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: 0.010 Normalize map: mean=0, sd=1: 4.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.990 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5880 Z= 0.277 Angle : 0.650 8.560 8220 Z= 0.457 Chirality : 0.048 0.198 934 Planarity : 0.007 0.109 836 Dihedral : 20.017 179.467 2531 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.37), residues: 543 helix: -0.16 (0.36), residues: 228 sheet: -1.08 (0.76), residues: 49 loop : -0.47 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 150 TYR 0.006 0.001 TYR A 140 PHE 0.014 0.001 PHE A 334 TRP 0.037 0.002 TRP A 249 HIS 0.002 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.28 ( 5880) covalent geometry : angle 0.65029 / 0.46 ( 8220) hydrogen bonds : bond 0.19072 / 12.35 ( 215) hydrogen bonds : angle 7.61631 / 5.68 ( 571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: A 303 ASP cc_start: 0.7760 (m-30) cc_final: 0.7473 (m-30) REVERT: A 405 LYS cc_start: 0.8066 (ttpp) cc_final: 0.7777 (ttpp) REVERT: A 582 GLU cc_start: 0.6350 (mm-30) cc_final: 0.6083 (mm-30) REVERT: A 585 ARG cc_start: 0.7591 (ttp-170) cc_final: 0.7334 (ttp80) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0886 time to fit residues: 10.6182 Evaluate side-chains 89 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 0.1980 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.0010 chunk 58 optimal weight: 3.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN A 393 GLN A 412 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.159277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.121521 restraints weight = 7788.500| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.56 r_work: 0.3325 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5880 Z= 0.171 Angle : 0.635 8.500 8220 Z= 0.340 Chirality : 0.046 0.183 934 Planarity : 0.007 0.070 836 Dihedral : 23.022 178.618 1410 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.64 % Allowed : 9.15 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.37), residues: 543 helix: -0.07 (0.34), residues: 237 sheet: -0.82 (0.66), residues: 63 loop : -0.47 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 106 TYR 0.008 0.001 TYR A 432 PHE 0.009 0.001 PHE A 635 TRP 0.023 0.001 TRP A 249 HIS 0.003 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 ( 5880) covalent geometry : angle 0.63471 / 0.34 ( 8220) hydrogen bonds : bond 0.05236 / 3.39 ( 215) hydrogen bonds : angle 4.97496 / 3.67 ( 571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 91 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: A 141 ASP cc_start: 0.7382 (m-30) cc_final: 0.7038 (m-30) REVERT: A 303 ASP cc_start: 0.8041 (m-30) cc_final: 0.7774 (m-30) REVERT: A 307 MET cc_start: 0.8323 (mtm) cc_final: 0.8083 (mtm) REVERT: A 405 LYS cc_start: 0.8530 (ttpp) cc_final: 0.8211 (tttm) REVERT: A 407 GLU cc_start: 0.6777 (tt0) cc_final: 0.6500 (tt0) REVERT: A 633 LYS cc_start: 0.7546 (ttpp) cc_final: 0.7344 (tttp) outliers start: 3 outliers final: 3 residues processed: 92 average time/residue: 0.0891 time to fit residues: 10.0090 Evaluate side-chains 91 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 321 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 53 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 43 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 0 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN A 412 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.157883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.119910 restraints weight = 7635.763| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.55 r_work: 0.3310 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5880 Z= 0.201 Angle : 0.623 9.278 8220 Z= 0.335 Chirality : 0.046 0.216 934 Planarity : 0.006 0.058 836 Dihedral : 23.204 178.392 1410 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.43 % Allowed : 13.83 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.37), residues: 543 helix: -0.18 (0.34), residues: 233 sheet: -0.97 (0.61), residues: 70 loop : -0.43 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 585 TYR 0.009 0.002 TYR A 140 PHE 0.012 0.001 PHE A 635 TRP 0.014 0.002 TRP A 249 HIS 0.003 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 ( 5880) covalent geometry : angle 0.62286 / 0.33 ( 8220) hydrogen bonds : bond 0.04843 / 3.20 ( 215) hydrogen bonds : angle 4.61929 / 3.40 ( 571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7741 (mt-10) REVERT: A 153 LYS cc_start: 0.7409 (mmmm) cc_final: 0.7120 (mmmm) REVERT: A 303 ASP cc_start: 0.8087 (m-30) cc_final: 0.7833 (m-30) REVERT: A 383 HIS cc_start: 0.7535 (t-170) cc_final: 0.7246 (t70) REVERT: A 405 LYS cc_start: 0.8550 (ttpp) cc_final: 0.8235 (tttm) REVERT: A 407 GLU cc_start: 0.6820 (tt0) cc_final: 0.6574 (tt0) REVERT: A 430 THR cc_start: 0.8163 (t) cc_final: 0.7896 (p) REVERT: A 583 THR cc_start: 0.7311 (m) cc_final: 0.7098 (m) REVERT: A 633 LYS cc_start: 0.7549 (ttpp) cc_final: 0.7291 (ttpp) outliers start: 2 outliers final: 2 residues processed: 91 average time/residue: 0.1003 time to fit residues: 11.1880 Evaluate side-chains 89 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 504 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 23 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 37 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN A 412 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.158245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.120680 restraints weight = 7753.694| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.48 r_work: 0.3322 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5880 Z= 0.174 Angle : 0.593 8.902 8220 Z= 0.320 Chirality : 0.045 0.227 934 Planarity : 0.006 0.052 836 Dihedral : 23.196 179.023 1410 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.70 % Allowed : 14.68 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.37), residues: 543 helix: -0.11 (0.34), residues: 233 sheet: -0.87 (0.61), residues: 70 loop : -0.40 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 574 TYR 0.008 0.001 TYR A 432 PHE 0.011 0.001 PHE A 635 TRP 0.016 0.002 TRP A 249 HIS 0.003 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 5880) covalent geometry : angle 0.59279 / 0.32 ( 8220) hydrogen bonds : bond 0.04264 / 2.80 ( 215) hydrogen bonds : angle 4.40455 / 3.25 ( 571) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.109 Fit side-chains revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7777 (mt-10) REVERT: A 153 LYS cc_start: 0.7462 (mmmm) cc_final: 0.7145 (mmmm) REVERT: A 303 ASP cc_start: 0.8050 (m-30) cc_final: 0.7823 (m-30) REVERT: A 383 HIS cc_start: 0.7417 (t-170) cc_final: 0.7162 (t70) REVERT: A 430 THR cc_start: 0.8194 (t) cc_final: 0.7931 (p) outliers start: 8 outliers final: 5 residues processed: 88 average time/residue: 0.0927 time to fit residues: 10.0088 Evaluate side-chains 88 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 504 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 20.0000 chunk 13 optimal weight: 0.1980 chunk 45 optimal weight: 7.9990 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN A 412 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.159540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.122333 restraints weight = 7755.249| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.51 r_work: 0.3336 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5880 Z= 0.160 Angle : 0.582 8.465 8220 Z= 0.314 Chirality : 0.044 0.237 934 Planarity : 0.006 0.050 836 Dihedral : 23.236 179.168 1410 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.28 % Allowed : 16.81 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.37), residues: 543 helix: -0.01 (0.35), residues: 232 sheet: -0.83 (0.61), residues: 70 loop : -0.43 (0.43), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 267 TYR 0.008 0.001 TYR A 432 PHE 0.009 0.001 PHE A 635 TRP 0.018 0.002 TRP A 249 HIS 0.003 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 ( 5880) covalent geometry : angle 0.58207 / 0.31 ( 8220) hydrogen bonds : bond 0.04041 / 2.65 ( 215) hydrogen bonds : angle 4.30226 / 3.18 ( 571) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.107 Fit side-chains revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7782 (mt-10) REVERT: A 303 ASP cc_start: 0.8050 (m-30) cc_final: 0.7829 (m-30) REVERT: A 383 HIS cc_start: 0.7362 (t-170) cc_final: 0.7102 (t70) REVERT: A 430 THR cc_start: 0.8211 (t) cc_final: 0.7947 (p) REVERT: A 433 ARG cc_start: 0.7311 (tpt170) cc_final: 0.6427 (ttt90) REVERT: A 633 LYS cc_start: 0.7565 (ttpp) cc_final: 0.7361 (ttpp) outliers start: 6 outliers final: 6 residues processed: 90 average time/residue: 0.0922 time to fit residues: 10.0697 Evaluate side-chains 91 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 504 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 0.0170 chunk 51 optimal weight: 0.0870 chunk 11 optimal weight: 0.0060 chunk 55 optimal weight: 3.9990 overall best weight: 0.2812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN A 412 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.160703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.123696 restraints weight = 7746.507| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.49 r_work: 0.3367 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5880 Z= 0.126 Angle : 0.552 7.641 8220 Z= 0.300 Chirality : 0.043 0.243 934 Planarity : 0.005 0.048 836 Dihedral : 23.201 178.828 1410 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.49 % Allowed : 17.66 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.37), residues: 543 helix: 0.14 (0.35), residues: 232 sheet: -0.52 (0.63), residues: 67 loop : -0.30 (0.43), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 267 TYR 0.007 0.001 TYR A 432 PHE 0.007 0.001 PHE A 635 TRP 0.016 0.001 TRP A 249 HIS 0.003 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 ( 5880) covalent geometry : angle 0.55194 / 0.30 ( 8220) hydrogen bonds : bond 0.03630 / 2.38 ( 215) hydrogen bonds : angle 4.12721 / 3.06 ( 571) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: A 303 ASP cc_start: 0.8033 (m-30) cc_final: 0.7800 (m-30) REVERT: A 383 HIS cc_start: 0.7321 (t-170) cc_final: 0.7062 (t70) REVERT: A 430 THR cc_start: 0.8201 (t) cc_final: 0.7931 (p) REVERT: A 433 ARG cc_start: 0.7290 (tpt170) cc_final: 0.6439 (ttt90) REVERT: A 633 LYS cc_start: 0.7512 (ttpp) cc_final: 0.7279 (ttpp) outliers start: 7 outliers final: 6 residues processed: 90 average time/residue: 0.0968 time to fit residues: 10.5660 Evaluate side-chains 89 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 504 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 52 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 0.2980 chunk 17 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN A 412 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.159300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.122109 restraints weight = 7761.623| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.49 r_work: 0.3339 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5880 Z= 0.186 Angle : 0.593 8.781 8220 Z= 0.319 Chirality : 0.045 0.240 934 Planarity : 0.006 0.049 836 Dihedral : 23.219 179.833 1410 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.91 % Allowed : 18.09 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.37), residues: 543 helix: 0.10 (0.35), residues: 233 sheet: -0.54 (0.63), residues: 67 loop : -0.28 (0.44), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 574 TYR 0.010 0.002 TYR A 432 PHE 0.011 0.001 PHE A 635 TRP 0.022 0.002 TRP A 249 HIS 0.003 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 ( 5880) covalent geometry : angle 0.59331 / 0.32 ( 8220) hydrogen bonds : bond 0.04042 / 2.67 ( 215) hydrogen bonds : angle 4.16523 / 3.08 ( 571) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 303 ASP cc_start: 0.8053 (m-30) cc_final: 0.7847 (m-30) REVERT: A 430 THR cc_start: 0.8218 (t) cc_final: 0.7968 (p) REVERT: A 433 ARG cc_start: 0.7307 (tpt170) cc_final: 0.6440 (ttt90) outliers start: 9 outliers final: 6 residues processed: 93 average time/residue: 0.0924 time to fit residues: 10.5128 Evaluate side-chains 91 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 504 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 4 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 41 optimal weight: 0.0770 chunk 57 optimal weight: 4.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS A 393 GLN A 412 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.159493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.122108 restraints weight = 7637.658| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.49 r_work: 0.3345 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5880 Z= 0.179 Angle : 0.610 10.383 8220 Z= 0.321 Chirality : 0.046 0.239 934 Planarity : 0.006 0.049 836 Dihedral : 23.229 179.802 1410 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.91 % Allowed : 19.15 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.37), residues: 543 helix: 0.04 (0.35), residues: 233 sheet: -0.56 (0.61), residues: 75 loop : -0.45 (0.44), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 403 TYR 0.008 0.001 TYR A 432 PHE 0.009 0.001 PHE A 350 TRP 0.023 0.002 TRP A 249 HIS 0.003 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 ( 5880) covalent geometry : angle 0.60998 / 0.32 ( 8220) hydrogen bonds : bond 0.03896 / 2.56 ( 215) hydrogen bonds : angle 4.18895 / 3.11 ( 571) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: A 303 ASP cc_start: 0.8062 (m-30) cc_final: 0.7855 (m-30) REVERT: A 430 THR cc_start: 0.8215 (t) cc_final: 0.7953 (p) REVERT: A 433 ARG cc_start: 0.7298 (tpt170) cc_final: 0.6455 (ttt90) outliers start: 9 outliers final: 7 residues processed: 94 average time/residue: 0.0911 time to fit residues: 10.3972 Evaluate side-chains 93 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 504 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 40 optimal weight: 20.0000 chunk 36 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 29 optimal weight: 0.0270 chunk 53 optimal weight: 0.6980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN A 412 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.160209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.123278 restraints weight = 7643.698| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.45 r_work: 0.3363 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5880 Z= 0.152 Angle : 0.596 10.862 8220 Z= 0.313 Chirality : 0.045 0.245 934 Planarity : 0.005 0.049 836 Dihedral : 23.211 179.841 1410 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.49 % Allowed : 20.00 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.37), residues: 543 helix: 0.11 (0.35), residues: 233 sheet: -0.54 (0.62), residues: 75 loop : -0.42 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.007 0.001 TYR A 432 PHE 0.009 0.001 PHE A 350 TRP 0.025 0.002 TRP A 249 HIS 0.008 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 5880) covalent geometry : angle 0.59593 / 0.31 ( 8220) hydrogen bonds : bond 0.03661 / 2.41 ( 215) hydrogen bonds : angle 4.10610 / 3.05 ( 571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7185 (pt) REVERT: A 303 ASP cc_start: 0.8021 (m-30) cc_final: 0.7799 (m-30) REVERT: A 430 THR cc_start: 0.8199 (t) cc_final: 0.7929 (p) outliers start: 7 outliers final: 6 residues processed: 92 average time/residue: 0.0870 time to fit residues: 9.9066 Evaluate side-chains 92 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 504 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 2 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 3 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN A 412 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.160303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.122485 restraints weight = 7809.143| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.51 r_work: 0.3359 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5880 Z= 0.153 Angle : 0.596 11.203 8220 Z= 0.313 Chirality : 0.045 0.246 934 Planarity : 0.005 0.049 836 Dihedral : 23.189 179.678 1410 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.70 % Allowed : 19.36 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.37), residues: 543 helix: 0.14 (0.35), residues: 233 sheet: -0.57 (0.63), residues: 75 loop : -0.41 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 267 TYR 0.008 0.001 TYR A 432 PHE 0.009 0.001 PHE A 635 TRP 0.027 0.002 TRP A 249 HIS 0.009 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 5880) covalent geometry : angle 0.59568 / 0.31 ( 8220) hydrogen bonds : bond 0.03611 / 2.38 ( 215) hydrogen bonds : angle 4.05109 / 3.00 ( 571) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7186 (pt) REVERT: A 303 ASP cc_start: 0.8030 (m-30) cc_final: 0.7805 (m-30) REVERT: A 430 THR cc_start: 0.8212 (t) cc_final: 0.7945 (p) outliers start: 8 outliers final: 6 residues processed: 92 average time/residue: 0.0976 time to fit residues: 10.9153 Evaluate side-chains 92 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 504 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.0670 chunk 12 optimal weight: 0.0970 chunk 3 optimal weight: 0.2980 chunk 49 optimal weight: 0.9990 chunk 25 optimal weight: 0.0770 chunk 52 optimal weight: 0.5980 chunk 38 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 overall best weight: 0.2274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN A 412 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.162360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.125506 restraints weight = 7761.483| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.50 r_work: 0.3387 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 5880 Z= 0.117 Angle : 0.561 10.962 8220 Z= 0.298 Chirality : 0.043 0.253 934 Planarity : 0.005 0.047 836 Dihedral : 23.179 179.377 1410 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.06 % Allowed : 20.21 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.38), residues: 543 helix: 0.27 (0.35), residues: 233 sheet: -0.48 (0.65), residues: 68 loop : -0.19 (0.43), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 260 TYR 0.007 0.001 TYR A 432 PHE 0.006 0.001 PHE A 350 TRP 0.030 0.002 TRP A 249 HIS 0.004 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 ( 5880) covalent geometry : angle 0.56081 / 0.30 ( 8220) hydrogen bonds : bond 0.03158 / 2.08 ( 215) hydrogen bonds : angle 3.90892 / 2.90 ( 571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1605.83 seconds wall clock time: 28 minutes 2.63 seconds (1682.63 seconds total)