Starting phenix.real_space_refine on Sat May 10 07:52:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrq_37786/05_2025/8wrq_37786.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrq_37786/05_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_37786/05_2025/8wrq_37786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrq_37786/05_2025/8wrq_37786.map" model { file = "/net/cci-nas-00/data/ceres_data/8wrq_37786/05_2025/8wrq_37786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrq_37786/05_2025/8wrq_37786.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.32, per 1000 atoms: 0.94 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: 1.43 Conformation dependent library (CDL) restraints added in 656.5 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: 1.81 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: 1.94 Time building geometry restraints manager: 1.67 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: 4.240 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.720 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.290 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.037 0.002 TRP A 249 HIS 0.002 0.001 HIS A 498 PHE 0.014 0.001 PHE A 334 TYR 0.006 0.001 TYR A 140 ARG 0.003 0.000 ARG A 150 Details of bonding type rmsd hydrogen bonds : bond 0.19072 ( 215) hydrogen bonds : angle 7.61631 ( 571) covalent geometry : bond 0.00316 ( 5880) covalent geometry : angle 0.56442 ( 8220) *********************** 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 : 0.566 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: 0.2638 time to fit residues: 31.7357 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 : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.9980 chunk 45 optimal weight: 20.0000 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.156850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.118912 restraints weight = 7610.361| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.53 r_work: 0.3296 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 5880 Z= 0.264 Angle : 0.663 10.230 8220 Z= 0.346 Chirality : 0.047 0.146 934 Planarity : 0.007 0.074 836 Dihedral : 23.256 178.087 1410 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.21 % Allowed : 9.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.36), residues: 543 helix: -0.19 (0.34), residues: 232 sheet: -0.68 (0.68), residues: 59 loop : -0.61 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 249 HIS 0.004 0.001 HIS A 135 PHE 0.016 0.002 PHE A 635 TYR 0.011 0.002 TYR A 140 ARG 0.004 0.001 ARG A 574 Details of bonding type rmsd hydrogen bonds : bond 0.04839 ( 215) hydrogen bonds : angle 4.90355 ( 571) covalent geometry : bond 0.00603 ( 5880) covalent geometry : angle 0.66320 ( 8220) *********************** 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: 1 poor density : 93 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: A 153 LYS cc_start: 0.7456 (mmmm) cc_final: 0.7173 (mmmm) REVERT: A 303 ASP cc_start: 0.8099 (m-30) cc_final: 0.7852 (m-30) REVERT: A 405 LYS cc_start: 0.8523 (ttpp) cc_final: 0.8213 (tttm) REVERT: A 407 GLU cc_start: 0.6925 (tt0) cc_final: 0.6677 (tt0) REVERT: A 582 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6833 (mm-30) REVERT: A 585 ARG cc_start: 0.8180 (ttp-170) cc_final: 0.7946 (ttp80) REVERT: A 633 LYS cc_start: 0.7532 (ttpp) cc_final: 0.7308 (ttpp) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.2660 time to fit residues: 29.6203 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 : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 51 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 46 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 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 138 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 = 0.3952 r_free = 0.3952 target = 0.158993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.121514 restraints weight = 7748.722| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.48 r_work: 0.3334 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1630 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 : 0.583 8.233 8220 Z= 0.304 Chirality : 0.043 0.135 934 Planarity : 0.006 0.060 836 Dihedral : 23.070 178.238 1410 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.28 % Allowed : 13.83 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.37), residues: 543 helix: -0.01 (0.35), residues: 233 sheet: -1.06 (0.61), residues: 71 loop : -0.44 (0.43), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 249 HIS 0.003 0.001 HIS A 498 PHE 0.009 0.001 PHE A 635 TYR 0.007 0.001 TYR A 432 ARG 0.003 0.000 ARG A 260 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 215) hydrogen bonds : angle 4.35934 ( 571) covalent geometry : bond 0.00406 ( 5880) covalent geometry : angle 0.58258 ( 8220) *********************** 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 101 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 153 LYS cc_start: 0.7422 (mmmm) cc_final: 0.7103 (mmmm) REVERT: A 303 ASP cc_start: 0.8050 (m-30) cc_final: 0.7835 (m-30) REVERT: A 383 HIS cc_start: 0.7324 (t-170) cc_final: 0.7070 (t70) REVERT: A 430 THR cc_start: 0.8171 (t) cc_final: 0.7926 (p) REVERT: A 433 ARG cc_start: 0.7313 (tpt170) cc_final: 0.6433 (ttt90) REVERT: A 633 LYS cc_start: 0.7545 (ttpp) cc_final: 0.7314 (ttpp) outliers start: 6 outliers final: 2 residues processed: 96 average time/residue: 0.2726 time to fit residues: 31.8840 Evaluate side-chains 91 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 347 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 5 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 48 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 27 optimal weight: 0.3980 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 44 optimal weight: 0.0000 chunk 43 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.3584 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.160934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.123291 restraints weight = 7791.825| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.52 r_work: 0.3369 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1883 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= 0.140 Angle : 0.551 7.213 8220 Z= 0.288 Chirality : 0.040 0.129 934 Planarity : 0.005 0.056 836 Dihedral : 23.153 178.478 1410 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.49 % Allowed : 15.74 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.38), residues: 543 helix: 0.26 (0.35), residues: 233 sheet: -0.71 (0.64), residues: 70 loop : -0.30 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 552 HIS 0.003 0.001 HIS A 498 PHE 0.007 0.001 PHE A 350 TYR 0.007 0.001 TYR A 432 ARG 0.006 0.000 ARG A 585 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 215) hydrogen bonds : angle 4.05920 ( 571) covalent geometry : bond 0.00315 ( 5880) covalent geometry : angle 0.55145 ( 8220) *********************** 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 101 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 153 LYS cc_start: 0.7418 (mmmm) cc_final: 0.7115 (mmmm) REVERT: A 303 ASP cc_start: 0.8001 (m-30) cc_final: 0.7777 (m-30) REVERT: A 383 HIS cc_start: 0.7207 (t-170) cc_final: 0.6929 (t70) REVERT: A 405 LYS cc_start: 0.8535 (ptmm) cc_final: 0.8275 (pttp) REVERT: A 430 THR cc_start: 0.8177 (t) cc_final: 0.7966 (p) REVERT: A 633 LYS cc_start: 0.7537 (ttpp) cc_final: 0.7326 (ttpp) outliers start: 7 outliers final: 4 residues processed: 99 average time/residue: 0.2585 time to fit residues: 31.2674 Evaluate side-chains 93 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 504 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 127 GLN A 138 ASN A 203 GLN A 383 HIS A 412 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.158814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.120335 restraints weight = 7665.613| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.50 r_work: 0.3327 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5880 Z= 0.209 Angle : 0.601 8.379 8220 Z= 0.314 Chirality : 0.044 0.189 934 Planarity : 0.006 0.054 836 Dihedral : 23.170 179.966 1410 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.13 % Allowed : 17.23 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.37), residues: 543 helix: 0.07 (0.34), residues: 233 sheet: -0.79 (0.60), residues: 78 loop : -0.50 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 249 HIS 0.003 0.001 HIS A 498 PHE 0.013 0.001 PHE A 635 TYR 0.009 0.002 TYR A 432 ARG 0.004 0.000 ARG A 574 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 215) hydrogen bonds : angle 4.27192 ( 571) covalent geometry : bond 0.00477 ( 5880) covalent geometry : angle 0.60068 ( 8220) *********************** 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 105 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 153 LYS cc_start: 0.7421 (mmmm) cc_final: 0.7156 (mmmm) REVERT: A 282 GLU cc_start: 0.7310 (tt0) cc_final: 0.7089 (mt-10) REVERT: A 303 ASP cc_start: 0.8045 (m-30) cc_final: 0.7839 (m-30) REVERT: A 405 LYS cc_start: 0.8529 (ptmm) cc_final: 0.8266 (pttp) REVERT: A 430 THR cc_start: 0.8219 (t) cc_final: 0.7959 (p) outliers start: 10 outliers final: 7 residues processed: 100 average time/residue: 0.2359 time to fit residues: 28.7325 Evaluate side-chains 102 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 351 THR Chi-restraints excluded: chain A residue 383 HIS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 55 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 0.0770 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.159280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.120885 restraints weight = 7631.343| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.48 r_work: 0.3337 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 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 : 0.004 0.034 5880 Z= 0.191 Angle : 0.585 8.125 8220 Z= 0.305 Chirality : 0.043 0.132 934 Planarity : 0.006 0.053 836 Dihedral : 23.136 179.768 1410 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.13 % Allowed : 18.30 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.37), residues: 543 helix: 0.09 (0.35), residues: 229 sheet: -0.71 (0.60), residues: 78 loop : -0.52 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 249 HIS 0.005 0.001 HIS A 383 PHE 0.010 0.001 PHE A 635 TYR 0.008 0.001 TYR A 432 ARG 0.006 0.000 ARG A 150 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 215) hydrogen bonds : angle 4.17771 ( 571) covalent geometry : bond 0.00436 ( 5880) covalent geometry : angle 0.58466 ( 8220) *********************** 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 100 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 153 LYS cc_start: 0.7421 (mmmm) cc_final: 0.7181 (mmmm) REVERT: A 303 ASP cc_start: 0.8056 (m-30) cc_final: 0.7850 (m-30) REVERT: A 405 LYS cc_start: 0.8537 (ptmm) cc_final: 0.8261 (pttp) REVERT: A 430 THR cc_start: 0.8211 (t) cc_final: 0.7942 (p) outliers start: 10 outliers final: 8 residues processed: 97 average time/residue: 0.2577 time to fit residues: 30.1648 Evaluate side-chains 100 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 26 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 HIS A 412 GLN A 577 ASN 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 = 0.157907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.119073 restraints weight = 7704.241| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.54 r_work: 0.3297 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 5880 Z= 0.254 Angle : 0.630 9.183 8220 Z= 0.328 Chirality : 0.046 0.147 934 Planarity : 0.006 0.054 836 Dihedral : 23.103 179.113 1410 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.98 % Allowed : 18.94 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.36), residues: 543 helix: -0.08 (0.35), residues: 230 sheet: -1.21 (0.61), residues: 72 loop : -0.67 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 249 HIS 0.004 0.001 HIS A 383 PHE 0.013 0.002 PHE A 635 TYR 0.011 0.002 TYR A 140 ARG 0.007 0.000 ARG A 150 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 215) hydrogen bonds : angle 4.39249 ( 571) covalent geometry : bond 0.00580 ( 5880) covalent geometry : angle 0.62988 ( 8220) *********************** 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 106 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 282 GLU cc_start: 0.7282 (tt0) cc_final: 0.7061 (mt-10) REVERT: A 303 ASP cc_start: 0.8089 (m-30) cc_final: 0.7862 (m-30) REVERT: A 405 LYS cc_start: 0.8568 (ptmm) cc_final: 0.8261 (pttp) REVERT: A 430 THR cc_start: 0.8226 (t) cc_final: 0.7932 (p) outliers start: 14 outliers final: 9 residues processed: 102 average time/residue: 0.2400 time to fit residues: 29.8787 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 : 0.529 ------------------------------------------------------------------------------- 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 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 416 LEU 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 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 38 optimal weight: 8.9990 chunk 2 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.3963 r_free = 0.3963 target = 0.159875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.121734 restraints weight = 7571.615| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.48 r_work: 0.3348 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2273 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= 0.163 Angle : 0.577 7.709 8220 Z= 0.298 Chirality : 0.042 0.147 934 Planarity : 0.006 0.053 836 Dihedral : 22.971 179.338 1410 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.13 % Allowed : 19.79 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.37), residues: 543 helix: 0.09 (0.35), residues: 231 sheet: -0.55 (0.61), residues: 75 loop : -0.48 (0.43), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 249 HIS 0.008 0.001 HIS A 383 PHE 0.009 0.001 PHE A 635 TYR 0.007 0.001 TYR A 432 ARG 0.002 0.000 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.03489 ( 215) hydrogen bonds : angle 4.11592 ( 571) covalent geometry : bond 0.00369 ( 5880) covalent geometry : angle 0.57666 ( 8220) *********************** 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 104 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 282 GLU cc_start: 0.7277 (tt0) cc_final: 0.7057 (mt-10) REVERT: A 303 ASP cc_start: 0.8021 (m-30) cc_final: 0.7802 (m-30) REVERT: A 405 LYS cc_start: 0.8479 (ptmm) cc_final: 0.8218 (pttp) REVERT: A 430 THR cc_start: 0.8227 (t) cc_final: 0.7950 (p) outliers start: 10 outliers final: 7 residues processed: 101 average time/residue: 0.2520 time to fit residues: 30.7764 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 : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 411 LEU 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 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 25 optimal weight: 0.0030 chunk 32 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3954 r_free = 0.3954 target = 0.159384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.120846 restraints weight = 7658.912| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.50 r_work: 0.3324 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2345 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= 0.186 Angle : 0.589 7.739 8220 Z= 0.304 Chirality : 0.043 0.181 934 Planarity : 0.006 0.052 836 Dihedral : 22.939 178.626 1410 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.70 % Allowed : 19.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.37), residues: 543 helix: 0.10 (0.35), residues: 229 sheet: -1.31 (0.60), residues: 72 loop : -0.52 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 249 HIS 0.010 0.001 HIS A 383 PHE 0.009 0.001 PHE A 635 TYR 0.009 0.001 TYR A 432 ARG 0.002 0.000 ARG A 574 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 215) hydrogen bonds : angle 4.14792 ( 571) covalent geometry : bond 0.00424 ( 5880) covalent geometry : angle 0.58915 ( 8220) *********************** 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: 8 poor density : 87 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 282 GLU cc_start: 0.7307 (tt0) cc_final: 0.7075 (mt-10) REVERT: A 303 ASP cc_start: 0.8032 (m-30) cc_final: 0.7808 (m-30) REVERT: A 405 LYS cc_start: 0.8481 (ptmm) cc_final: 0.8215 (pttp) REVERT: A 430 THR cc_start: 0.8224 (t) cc_final: 0.7949 (p) outliers start: 8 outliers final: 8 residues processed: 92 average time/residue: 0.2465 time to fit residues: 27.4520 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 : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 411 LEU 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 3 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 0.0670 chunk 32 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.159555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.121259 restraints weight = 7728.063| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.51 r_work: 0.3323 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2370 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= 0.188 Angle : 0.589 7.726 8220 Z= 0.304 Chirality : 0.043 0.177 934 Planarity : 0.006 0.052 836 Dihedral : 22.925 178.726 1410 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.70 % Allowed : 19.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.37), residues: 543 helix: 0.10 (0.35), residues: 231 sheet: -1.35 (0.60), residues: 72 loop : -0.53 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 249 HIS 0.009 0.001 HIS A 383 PHE 0.010 0.001 PHE A 635 TYR 0.009 0.001 TYR A 432 ARG 0.002 0.000 ARG A 574 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 215) hydrogen bonds : angle 4.12990 ( 571) covalent geometry : bond 0.00428 ( 5880) covalent geometry : angle 0.58889 ( 8220) ********************** 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 95 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 282 GLU cc_start: 0.7304 (tt0) cc_final: 0.7072 (mt-10) REVERT: A 303 ASP cc_start: 0.8034 (m-30) cc_final: 0.7810 (m-30) REVERT: A 405 LYS cc_start: 0.8467 (ptmm) cc_final: 0.8200 (pttp) REVERT: A 430 THR cc_start: 0.8222 (t) cc_final: 0.7941 (p) outliers start: 8 outliers final: 7 residues processed: 92 average time/residue: 0.2608 time to fit residues: 28.9654 Evaluate side-chains 97 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 411 LEU 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 14 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 0.0670 chunk 2 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 1 optimal weight: 0.8980 overall best weight: 0.4118 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.160785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.122638 restraints weight = 7686.058| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.50 r_work: 0.3353 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2431 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= 0.149 Angle : 0.564 6.874 8220 Z= 0.291 Chirality : 0.041 0.167 934 Planarity : 0.005 0.051 836 Dihedral : 22.869 179.159 1410 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.37), residues: 543 helix: 0.20 (0.35), residues: 231 sheet: -1.26 (0.61), residues: 72 loop : -0.46 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 249 HIS 0.009 0.001 HIS A 383 PHE 0.008 0.001 PHE A 635 TYR 0.007 0.001 TYR A 432 ARG 0.002 0.000 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.03300 ( 215) hydrogen bonds : angle 4.02382 ( 571) covalent geometry : bond 0.00339 ( 5880) covalent geometry : angle 0.56360 ( 8220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4069.30 seconds wall clock time: 71 minutes 21.50 seconds (4281.50 seconds total)