Starting phenix.real_space_refine on Fri Aug 22 16:06:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrq_37786/08_2025/8wrq_37786.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrq_37786/08_2025/8wrq_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_2025/8wrq_37786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrq_37786/08_2025/8wrq_37786.map" model { file = "/net/cci-nas-00/data/ceres_data/8wrq_37786/08_2025/8wrq_37786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrq_37786/08_2025/8wrq_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-2.0-5787/lib/python3.9/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: 1.72, per 1000 atoms: 0.31 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: 0.42 Conformation dependent library (CDL) restraints added in 240.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.53 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: 0.91 Time building geometry restraints manager: 0.55 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=" O3' U B -10 " pdb=" P U B -9 " ideal model delta sigma weight residual 1.607 1.629 -0.022 1.50e-02 4.44e+03 2.17e+00 bond pdb=" O3' DG D -8 " pdb=" P DG D -7 " ideal model delta sigma weight residual 1.607 1.627 -0.020 1.50e-02 4.44e+03 1.79e+00 bond pdb=" O3' C B 8 " pdb=" P G B 9 " ideal model delta sigma weight residual 1.607 1.627 -0.020 1.50e-02 4.44e+03 1.77e+00 bond pdb=" CG PRO A 119 " pdb=" CD PRO A 119 " ideal model delta sigma weight residual 1.503 1.546 -0.043 3.40e-02 8.65e+02 1.62e+00 bond pdb=" O3' U B -9 " pdb=" P C B -8 " ideal model delta sigma weight residual 1.607 1.625 -0.018 1.50e-02 4.44e+03 1.49e+00 ... (remaining 5875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 8030 1.71 - 3.42: 167 3.42 - 5.14: 20 5.14 - 6.85: 2 6.85 - 8.56: 1 Bond angle restraints: 8220 Sorted by residual: angle pdb=" CA PRO A 119 " pdb=" N PRO A 119 " pdb=" CD PRO A 119 " ideal model delta sigma weight residual 112.00 107.87 4.13 1.40e+00 5.10e-01 8.69e+00 angle pdb=" C4' DG D -8 " pdb=" C3' DG D -8 " pdb=" O3' DG D -8 " ideal model delta sigma weight residual 110.00 113.91 -3.91 1.50e+00 4.44e-01 6.80e+00 angle pdb=" C3' DG D -8 " pdb=" C2' DG D -8 " pdb=" C1' DG D -8 " ideal model delta sigma weight residual 101.60 105.15 -3.55 1.50e+00 4.44e-01 5.59e+00 angle pdb=" C GLU A 486 " pdb=" N LYS A 487 " pdb=" CA LYS A 487 " ideal model delta sigma weight residual 121.54 125.92 -4.38 1.91e+00 2.74e-01 5.26e+00 angle pdb=" C3' DG D -8 " pdb=" O3' DG D -8 " pdb=" P DG D -7 " ideal model delta sigma weight residual 120.20 123.51 -3.31 1.50e+00 4.44e-01 4.88e+00 ... (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 - 0.028: 571 0.028 - 0.055: 222 0.055 - 0.083: 89 0.083 - 0.111: 35 0.111 - 0.139: 17 Chirality restraints: 934 Sorted by residual: 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=" CA ILE A 238 " pdb=" N ILE A 238 " pdb=" C ILE A 238 " pdb=" CB ILE A 238 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 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 -2.66 -2.53 -0.13 2.00e-01 2.50e+01 4.09e-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: 0.000 Normalize map: mean=0, sd=1: 3.970 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: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.480 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 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 : 0.003 0.045 5880 Z= 0.143 Angle : 0.564 8.560 8220 Z= 0.303 Chirality : 0.040 0.139 934 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 aren 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 covalent geometry : bond 0.00316 ( 5880) covalent geometry : angle 0.56442 ( 8220) hydrogen bonds : bond 0.19072 ( 215) hydrogen bonds : angle 7.61631 ( 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 : 0.193 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: 0.1140 time to fit residues: 13.5800 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 : 0.182 ------------------------------------------------------------------------------- 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: 1.9990 chunk 24 optimal weight: 0.1980 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 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: 0.3980 chunk 58 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3947 r_free = 0.3947 target = 0.158741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.120907 restraints weight = 7794.237| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.56 r_work: 0.3321 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1303 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= 0.189 Angle : 0.611 9.099 8220 Z= 0.319 Chirality : 0.044 0.147 934 Planarity : 0.007 0.074 836 Dihedral : 23.201 177.001 1410 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % 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 aren not related in a simple way. whole: -0.59 (0.37), residues: 543 helix: -0.05 (0.35), residues: 233 sheet: -0.78 (0.67), residues: 63 loop : -0.46 (0.42), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 642 TYR 0.008 0.001 TYR A 432 PHE 0.012 0.001 PHE A 635 TRP 0.021 0.002 TRP A 249 HIS 0.003 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 5880) covalent geometry : angle 0.61147 ( 8220) hydrogen bonds : bond 0.04409 ( 215) hydrogen bonds : angle 4.74289 ( 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 93 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 153 LYS cc_start: 0.7431 (mmmm) cc_final: 0.7138 (mmmm) REVERT: A 303 ASP cc_start: 0.8099 (m-30) cc_final: 0.7851 (m-30) REVERT: A 430 THR cc_start: 0.8136 (t) cc_final: 0.7900 (p) REVERT: A 633 LYS cc_start: 0.7548 (ttpp) cc_final: 0.7331 (ttpp) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1223 time to fit residues: 13.7088 Evaluate side-chains 86 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 35 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 0 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3937 r_free = 0.3937 target = 0.157603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.119865 restraints weight = 7522.397| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.49 r_work: 0.3312 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 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 : 0.006 0.044 5880 Z= 0.250 Angle : 0.635 9.646 8220 Z= 0.331 Chirality : 0.046 0.149 934 Planarity : 0.007 0.062 836 Dihedral : 23.183 178.984 1410 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.28 % Allowed : 13.40 % Favored : 85.32 % 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 aren not related in a simple way. whole: -0.90 (0.36), residues: 543 helix: -0.12 (0.34), residues: 232 sheet: -1.07 (0.59), residues: 78 loop : -0.74 (0.42), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 585 TYR 0.011 0.002 TYR A 140 PHE 0.014 0.002 PHE A 635 TRP 0.015 0.002 TRP A 249 HIS 0.003 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00572 ( 5880) covalent geometry : angle 0.63472 ( 8220) hydrogen bonds : bond 0.04487 ( 215) hydrogen bonds : angle 4.62944 ( 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 95 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7809 (mt-10) REVERT: A 153 LYS cc_start: 0.7425 (mmmm) cc_final: 0.7115 (mmmm) REVERT: A 303 ASP cc_start: 0.8035 (m-30) cc_final: 0.7824 (m-30) REVERT: A 433 ARG cc_start: 0.7319 (tpt170) cc_final: 0.6454 (ttt90) outliers start: 6 outliers final: 3 residues processed: 90 average time/residue: 0.1305 time to fit residues: 13.9251 Evaluate side-chains 93 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 414 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN A 412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.157632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.119151 restraints weight = 7693.961| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.52 r_work: 0.3305 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 5880 Z= 0.243 Angle : 0.628 9.272 8220 Z= 0.328 Chirality : 0.045 0.159 934 Planarity : 0.006 0.061 836 Dihedral : 23.209 179.923 1410 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.70 % Allowed : 16.17 % Favored : 82.13 % 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 aren not related in a simple way. whole: -0.84 (0.37), residues: 543 helix: -0.09 (0.35), residues: 232 sheet: -1.03 (0.59), residues: 78 loop : -0.70 (0.42), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 574 TYR 0.010 0.002 TYR A 140 PHE 0.012 0.001 PHE A 635 TRP 0.024 0.002 TRP A 552 HIS 0.003 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00555 ( 5880) covalent geometry : angle 0.62782 ( 8220) hydrogen bonds : bond 0.04252 ( 215) hydrogen bonds : angle 4.42498 ( 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 104 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 153 LYS cc_start: 0.7432 (mmmm) cc_final: 0.7153 (mmmm) REVERT: A 303 ASP cc_start: 0.8084 (m-30) cc_final: 0.7873 (m-30) REVERT: A 430 THR cc_start: 0.8201 (t) cc_final: 0.7940 (p) outliers start: 8 outliers final: 5 residues processed: 100 average time/residue: 0.1074 time to fit residues: 13.0828 Evaluate side-chains 95 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 280 LEU 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: 0.0980 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 42 optimal weight: 20.0000 chunk 13 optimal weight: 0.0980 chunk 45 optimal weight: 8.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 ASN A 138 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS A 412 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.160797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.123567 restraints weight = 7772.768| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.51 r_work: 0.3360 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5880 Z= 0.142 Angle : 0.553 7.040 8220 Z= 0.289 Chirality : 0.041 0.130 934 Planarity : 0.005 0.057 836 Dihedral : 23.161 179.327 1410 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.49 % Allowed : 17.45 % Favored : 81.06 % 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 aren not related in a simple way. whole: -0.28 (0.38), residues: 543 helix: 0.25 (0.35), residues: 232 sheet: -0.70 (0.64), residues: 68 loop : -0.30 (0.43), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 150 TYR 0.007 0.001 TYR A 432 PHE 0.007 0.001 PHE A 350 TRP 0.016 0.001 TRP A 249 HIS 0.003 0.001 HIS A 498 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 5880) covalent geometry : angle 0.55278 ( 8220) hydrogen bonds : bond 0.03288 ( 215) hydrogen bonds : angle 4.04589 ( 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 96 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7192 (pt) REVERT: A 303 ASP cc_start: 0.8047 (m-30) cc_final: 0.7843 (m-30) REVERT: A 430 THR cc_start: 0.8167 (t) cc_final: 0.7951 (p) outliers start: 7 outliers final: 4 residues processed: 94 average time/residue: 0.1172 time to fit residues: 13.3062 Evaluate side-chains 92 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 383 HIS 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: 0.9990 chunk 53 optimal weight: 0.0050 chunk 56 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 0.0670 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.5132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.159864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.122095 restraints weight = 7780.719| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.51 r_work: 0.3340 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2115 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= 0.171 Angle : 0.568 7.174 8220 Z= 0.295 Chirality : 0.042 0.166 934 Planarity : 0.006 0.053 836 Dihedral : 23.095 179.806 1410 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.55 % Allowed : 17.02 % Favored : 80.43 % 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 aren not related in a simple way. whole: -0.43 (0.37), residues: 543 helix: 0.17 (0.35), residues: 235 sheet: -0.64 (0.61), residues: 75 loop : -0.47 (0.44), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 150 TYR 0.008 0.001 TYR A 432 PHE 0.008 0.001 PHE A 635 TRP 0.018 0.001 TRP A 249 HIS 0.003 0.001 HIS A 498 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 5880) covalent geometry : angle 0.56801 ( 8220) hydrogen bonds : bond 0.03485 ( 215) hydrogen bonds : angle 4.04783 ( 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 111 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7126 (pt) REVERT: A 282 GLU cc_start: 0.7272 (tt0) cc_final: 0.7052 (mt-10) REVERT: A 303 ASP cc_start: 0.8031 (m-30) cc_final: 0.7808 (m-30) REVERT: A 405 LYS cc_start: 0.8547 (ptmm) cc_final: 0.8272 (pttp) REVERT: A 430 THR cc_start: 0.8211 (t) cc_final: 0.7962 (p) outliers start: 12 outliers final: 7 residues processed: 107 average time/residue: 0.1156 time to fit residues: 14.8761 Evaluate side-chains 103 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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 280 LEU 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 426 VAL 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: 0.9980 chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 chunk 50 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 38 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 138 ASN 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 = 0.159512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.121697 restraints weight = 7753.955| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.50 r_work: 0.3332 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2193 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= 0.180 Angle : 0.575 7.323 8220 Z= 0.299 Chirality : 0.042 0.152 934 Planarity : 0.006 0.052 836 Dihedral : 22.969 179.400 1410 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.13 % Allowed : 17.66 % Favored : 80.21 % 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 aren not related in a simple way. whole: -0.44 (0.37), residues: 543 helix: 0.16 (0.35), residues: 235 sheet: -0.63 (0.60), residues: 75 loop : -0.47 (0.43), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 150 TYR 0.008 0.001 TYR A 432 PHE 0.009 0.001 PHE A 635 TRP 0.020 0.001 TRP A 249 HIS 0.009 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 5880) covalent geometry : angle 0.57488 ( 8220) hydrogen bonds : bond 0.03608 ( 215) hydrogen bonds : angle 4.07713 ( 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 101 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 282 GLU cc_start: 0.7283 (tt0) cc_final: 0.7054 (mt-10) REVERT: A 303 ASP cc_start: 0.8041 (m-30) cc_final: 0.7813 (m-30) REVERT: A 405 LYS cc_start: 0.8541 (ptmm) cc_final: 0.8261 (pttp) REVERT: A 430 THR cc_start: 0.8245 (t) cc_final: 0.7966 (p) outliers start: 10 outliers final: 9 residues processed: 99 average time/residue: 0.1107 time to fit residues: 13.2801 Evaluate side-chains 99 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.187 ------------------------------------------------------------------------------- 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 280 LEU 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 426 VAL 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: 0.0170 chunk 0 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 45 optimal weight: 0.0980 chunk 24 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 overall best weight: 0.3018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 GLN A 577 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.161454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.123788 restraints weight = 7627.847| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.48 r_work: 0.3373 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5880 Z= 0.127 Angle : 0.538 6.147 8220 Z= 0.280 Chirality : 0.040 0.133 934 Planarity : 0.005 0.051 836 Dihedral : 22.873 179.930 1410 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.34 % Allowed : 17.87 % Favored : 79.79 % 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 aren not related in a simple way. whole: -0.11 (0.38), residues: 543 helix: 0.33 (0.35), residues: 233 sheet: -0.41 (0.63), residues: 67 loop : -0.21 (0.43), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 150 TYR 0.007 0.001 TYR A 432 PHE 0.007 0.001 PHE A 635 TRP 0.022 0.001 TRP A 249 HIS 0.007 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 5880) covalent geometry : angle 0.53834 ( 8220) hydrogen bonds : bond 0.03091 ( 215) hydrogen bonds : angle 3.87691 ( 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 96 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7053 (pt) REVERT: A 282 GLU cc_start: 0.7224 (tt0) cc_final: 0.6999 (mt-10) REVERT: A 303 ASP cc_start: 0.8029 (m-30) cc_final: 0.7789 (m-30) REVERT: A 377 MET cc_start: 0.7601 (ttm) cc_final: 0.7370 (ttp) REVERT: A 405 LYS cc_start: 0.8467 (ptmm) cc_final: 0.8190 (pttp) REVERT: A 430 THR cc_start: 0.8183 (t) cc_final: 0.7937 (p) outliers start: 11 outliers final: 9 residues processed: 92 average time/residue: 0.1255 time to fit residues: 13.9343 Evaluate side-chains 95 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 280 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 426 VAL 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: 0.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 7 optimal weight: 0.0670 chunk 40 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 14 optimal weight: 0.1980 chunk 29 optimal weight: 0.6980 chunk 53 optimal weight: 0.0970 overall best weight: 0.2716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.161658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.125024 restraints weight = 7817.747| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.50 r_work: 0.3378 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5880 Z= 0.122 Angle : 0.526 5.906 8220 Z= 0.273 Chirality : 0.039 0.126 934 Planarity : 0.005 0.050 836 Dihedral : 22.765 179.914 1410 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.13 % Allowed : 18.72 % Favored : 79.15 % 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 aren not related in a simple way. whole: 0.06 (0.38), residues: 543 helix: 0.46 (0.35), residues: 233 sheet: -0.18 (0.63), residues: 67 loop : -0.15 (0.44), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 150 TYR 0.007 0.001 TYR A 432 PHE 0.006 0.001 PHE A 635 TRP 0.023 0.001 TRP A 249 HIS 0.007 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 5880) covalent geometry : angle 0.52563 ( 8220) hydrogen bonds : bond 0.02934 ( 215) hydrogen bonds : angle 3.74842 ( 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 95 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6992 (pt) REVERT: A 282 GLU cc_start: 0.7173 (tt0) cc_final: 0.6951 (mt-10) REVERT: A 303 ASP cc_start: 0.8017 (m-30) cc_final: 0.7775 (m-30) REVERT: A 405 LYS cc_start: 0.8431 (ptmm) cc_final: 0.8164 (pttp) REVERT: A 430 THR cc_start: 0.8154 (t) cc_final: 0.7929 (p) outliers start: 10 outliers final: 6 residues processed: 92 average time/residue: 0.1047 time to fit residues: 11.6807 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 : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 280 LEU 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 426 VAL 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: 1.9990 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 0.0870 chunk 2 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 1 optimal weight: 0.4980 chunk 37 optimal weight: 0.3980 chunk 3 optimal weight: 0.2980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.161053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.123937 restraints weight = 7924.092| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.53 r_work: 0.3365 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5880 Z= 0.133 Angle : 0.537 6.496 8220 Z= 0.278 Chirality : 0.040 0.152 934 Planarity : 0.005 0.049 836 Dihedral : 22.746 179.974 1410 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.70 % Allowed : 18.94 % Favored : 79.36 % 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 aren not related in a simple way. whole: 0.03 (0.38), residues: 543 helix: 0.46 (0.35), residues: 235 sheet: -0.19 (0.63), residues: 67 loop : -0.19 (0.44), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 150 TYR 0.007 0.001 TYR A 432 PHE 0.008 0.001 PHE A 635 TRP 0.027 0.001 TRP A 249 HIS 0.006 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 5880) covalent geometry : angle 0.53671 ( 8220) hydrogen bonds : bond 0.03084 ( 215) hydrogen bonds : angle 3.77074 ( 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 93 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7008 (pt) REVERT: A 303 ASP cc_start: 0.8075 (m-30) cc_final: 0.7818 (m-30) REVERT: A 430 THR cc_start: 0.8152 (t) cc_final: 0.7891 (p) outliers start: 8 outliers final: 7 residues processed: 91 average time/residue: 0.1096 time to fit residues: 12.0281 Evaluate side-chains 93 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 426 VAL 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: 0.0970 chunk 11 optimal weight: 0.0020 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.0670 chunk 12 optimal weight: 0.1980 chunk 3 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 chunk 25 optimal weight: 0.0040 chunk 52 optimal weight: 0.1980 chunk 38 optimal weight: 8.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.0736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.165038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.128886 restraints weight = 7876.906| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.52 r_work: 0.3436 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 5880 Z= 0.101 Angle : 0.509 6.734 8220 Z= 0.265 Chirality : 0.038 0.132 934 Planarity : 0.005 0.049 836 Dihedral : 22.669 178.058 1410 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.49 % Allowed : 19.36 % Favored : 79.15 % 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 aren not related in a simple way. whole: 0.29 (0.38), residues: 543 helix: 0.68 (0.36), residues: 234 sheet: 0.05 (0.65), residues: 67 loop : -0.09 (0.44), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 150 TYR 0.006 0.001 TYR A 432 PHE 0.004 0.001 PHE A 137 TRP 0.027 0.001 TRP A 249 HIS 0.005 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 5880) covalent geometry : angle 0.50941 ( 8220) hydrogen bonds : bond 0.02510 ( 215) hydrogen bonds : angle 3.60393 ( 571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2042.25 seconds wall clock time: 35 minutes 30.94 seconds (2130.94 seconds total)