Starting phenix.real_space_refine on Tue Feb 11 01:34:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ru4_24696/02_2025/7ru4_24696.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ru4_24696/02_2025/7ru4_24696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ru4_24696/02_2025/7ru4_24696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ru4_24696/02_2025/7ru4_24696.map" model { file = "/net/cci-nas-00/data/ceres_data/7ru4_24696/02_2025/7ru4_24696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ru4_24696/02_2025/7ru4_24696.cif" } resolution = 3.3 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= 0.016 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: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2151 2.51 5 N 564 2.21 5 O 653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3382 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 894 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 826 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1610 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 1 Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.12, per 1000 atoms: 1.22 Number of scatterers: 3382 At special positions: 0 Unit cell: (64.89, 99.91, 84.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 653 8.00 N 564 7.00 C 2151 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " BETA1-6 " NAG B 1 " - " FUC B 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG B 1 " - " ASN A 343 " Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 411.8 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 9 sheets defined 15.0% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.799A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.899A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.233A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.886A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.208A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 9 through 11 removed outlier: 4.048A pdb=" N ALA H 9 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR H 110 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 9 through 11 removed outlier: 4.048A pdb=" N ALA H 9 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR H 110 " --> pdb=" O ALA H 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.482A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.500A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 127 hydrogen bonds defined for protein. 297 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.99 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 949 1.33 - 1.47: 1110 1.47 - 1.61: 1385 1.61 - 1.74: 4 1.74 - 1.88: 16 Bond restraints: 3464 Sorted by residual: bond pdb=" CB ILE A 326 " pdb=" CG1 ILE A 326 " ideal model delta sigma weight residual 1.530 1.679 -0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" CG GLN L 6 " pdb=" CD GLN L 6 " ideal model delta sigma weight residual 1.516 1.384 0.132 2.50e-02 1.60e+03 2.79e+01 bond pdb=" CB TYR L 87 " pdb=" CG TYR L 87 " ideal model delta sigma weight residual 1.512 1.397 0.115 2.20e-02 2.07e+03 2.75e+01 bond pdb=" CB TYR L 36 " pdb=" CG TYR L 36 " ideal model delta sigma weight residual 1.512 1.398 0.114 2.20e-02 2.07e+03 2.67e+01 bond pdb=" CB ILE A 472 " pdb=" CG2 ILE A 472 " ideal model delta sigma weight residual 1.521 1.363 0.158 3.30e-02 9.18e+02 2.29e+01 ... (remaining 3459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 4038 2.58 - 5.15: 576 5.15 - 7.73: 72 7.73 - 10.30: 16 10.30 - 12.88: 4 Bond angle restraints: 4706 Sorted by residual: angle pdb=" N ARG L 61 " pdb=" CA ARG L 61 " pdb=" C ARG L 61 " ideal model delta sigma weight residual 114.56 101.68 12.88 1.27e+00 6.20e-01 1.03e+02 angle pdb=" N ALA A 520 " pdb=" CA ALA A 520 " pdb=" C ALA A 520 " ideal model delta sigma weight residual 108.13 117.09 -8.96 9.00e-01 1.23e+00 9.91e+01 angle pdb=" N LEU H 54 " pdb=" CA LEU H 54 " pdb=" C LEU H 54 " ideal model delta sigma weight residual 113.97 102.00 11.97 1.28e+00 6.10e-01 8.75e+01 angle pdb=" N GLN A 474 " pdb=" CA GLN A 474 " pdb=" C GLN A 474 " ideal model delta sigma weight residual 110.55 122.38 -11.83 1.35e+00 5.49e-01 7.68e+01 angle pdb=" N PHE L 98 " pdb=" CA PHE L 98 " pdb=" C PHE L 98 " ideal model delta sigma weight residual 113.30 124.82 -11.52 1.34e+00 5.57e-01 7.39e+01 ... (remaining 4701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.72: 1998 14.72 - 29.45: 69 29.45 - 44.17: 15 44.17 - 58.90: 13 58.90 - 73.62: 4 Dihedral angle restraints: 2099 sinusoidal: 864 harmonic: 1235 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 138.11 -45.11 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 64.13 28.87 1 1.00e+01 1.00e-02 1.19e+01 dihedral pdb=" SG CYS A 391 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " pdb=" CA CYS A 525 " ideal model delta sinusoidal sigma weight residual 79.00 23.24 55.76 1 2.00e+01 2.50e-03 1.05e+01 ... (remaining 2096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 322 0.087 - 0.173: 141 0.173 - 0.260: 46 0.260 - 0.346: 11 0.346 - 0.433: 6 Chirality restraints: 526 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.08e+02 chirality pdb=" C1 FUC B 3 " pdb=" O6 NAG B 1 " pdb=" C2 FUC B 3 " pdb=" O5 FUC B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.98e+01 chirality pdb=" C2 NAG B 2 " pdb=" C1 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" N2 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.92 0.43 2.00e-01 2.50e+01 4.68e+00 ... (remaining 523 not shown) Planarity restraints: 599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " -0.057 2.00e-02 2.50e+03 2.67e-02 1.78e+01 pdb=" CG TRP H 47 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " 0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " 0.026 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " -0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 32 " -0.056 2.00e-02 2.50e+03 2.94e-02 1.73e+01 pdb=" CG TYR L 32 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR L 32 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR L 32 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR L 32 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR L 32 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR L 32 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR L 32 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 478 " 0.018 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C THR A 478 " -0.060 2.00e-02 2.50e+03 pdb=" O THR A 478 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO A 479 " 0.020 2.00e-02 2.50e+03 ... (remaining 596 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1243 2.87 - 3.38: 2954 3.38 - 3.88: 5675 3.88 - 4.39: 6717 4.39 - 4.90: 10862 Nonbonded interactions: 27451 Sorted by model distance: nonbonded pdb=" OE1 GLU A 340 " pdb=" NZ LYS A 356 " model vdw 2.362 3.120 nonbonded pdb=" N LEU H 54 " pdb=" N ASP H 55 " model vdw 2.363 2.560 nonbonded pdb=" N ARG L 61 " pdb=" N PHE L 62 " model vdw 2.377 2.560 nonbonded pdb=" N PRO A 426 " pdb=" O PRO A 426 " model vdw 2.440 2.496 nonbonded pdb=" N GLN H 97 " pdb=" O GLN H 97 " model vdw 2.463 2.496 ... (remaining 27446 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: 3.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.650 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.010 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 0.023 0.158 3464 Z= 1.507 Angle : 1.894 12.879 4706 Z= 1.262 Chirality : 0.113 0.433 526 Planarity : 0.008 0.035 597 Dihedral : 9.651 73.619 1295 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.55 % Allowed : 1.10 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.06 (0.40), residues: 420 helix: -3.40 (0.59), residues: 31 sheet: 1.34 (0.44), residues: 150 loop : -0.30 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.010 TRP H 47 HIS 0.003 0.002 HIS L 90 PHE 0.026 0.005 PHE A 374 TYR 0.056 0.008 TYR L 32 ARG 0.005 0.001 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 120 time to evaluate : 0.367 Fit side-chains REVERT: H 89 VAL cc_start: 0.9153 (t) cc_final: 0.8894 (p) REVERT: A 332 ILE cc_start: 0.8865 (mt) cc_final: 0.8380 (mt) REVERT: A 336 CYS cc_start: 0.6290 (m) cc_final: 0.5884 (m) REVERT: A 360 ASN cc_start: 0.8823 (t0) cc_final: 0.8398 (t0) REVERT: A 453 TYR cc_start: 0.5598 (m-80) cc_final: 0.5330 (m-80) REVERT: A 458 LYS cc_start: 0.7751 (pttt) cc_final: 0.7151 (mmtm) outliers start: 2 outliers final: 0 residues processed: 122 average time/residue: 0.2487 time to fit residues: 34.5065 Evaluate side-chains 75 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.2980 chunk 31 optimal weight: 0.0970 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 97 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.087999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.081010 restraints weight = 9493.160| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.68 r_work: 0.3313 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3464 Z= 0.242 Angle : 0.747 10.120 4706 Z= 0.392 Chirality : 0.050 0.184 526 Planarity : 0.005 0.041 597 Dihedral : 5.821 25.559 549 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.11 % Allowed : 7.67 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.20 (0.40), residues: 420 helix: -1.67 (1.25), residues: 25 sheet: 0.83 (0.42), residues: 149 loop : -0.56 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.001 0.001 HIS L 90 PHE 0.009 0.001 PHE H 29 TYR 0.023 0.002 TYR A 495 ARG 0.006 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.389 Fit side-chains REVERT: H 100 LEU cc_start: 0.9360 (mt) cc_final: 0.9085 (mt) REVERT: L 21 LEU cc_start: 0.8975 (mm) cc_final: 0.8736 (mp) REVERT: A 328 ARG cc_start: 0.7624 (tpt90) cc_final: 0.4680 (pmt-80) REVERT: A 356 LYS cc_start: 0.8808 (tttt) cc_final: 0.7995 (tttt) REVERT: A 420 ASP cc_start: 0.6851 (m-30) cc_final: 0.6067 (t0) REVERT: A 458 LYS cc_start: 0.7875 (pttt) cc_final: 0.7036 (mmpt) REVERT: A 460 ASN cc_start: 0.6994 (m-40) cc_final: 0.6320 (m-40) outliers start: 15 outliers final: 7 residues processed: 100 average time/residue: 0.1671 time to fit residues: 20.1239 Evaluate side-chains 79 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 398 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 0.0170 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 37 optimal weight: 0.0020 chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.6030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 97 GLN H 105 GLN L 6 GLN L 100 GLN A 501 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.086612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.079360 restraints weight = 9339.948| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.70 r_work: 0.3280 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 3464 Z= 0.255 Angle : 0.677 7.750 4706 Z= 0.355 Chirality : 0.048 0.217 526 Planarity : 0.005 0.046 597 Dihedral : 5.516 28.663 549 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.38 % Allowed : 11.78 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.37 (0.40), residues: 420 helix: -1.84 (1.14), residues: 25 sheet: 0.87 (0.42), residues: 150 loop : -0.80 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS L 90 PHE 0.020 0.001 PHE A 497 TYR 0.018 0.002 TYR A 453 ARG 0.005 0.001 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.422 Fit side-chains REVERT: H 4 LEU cc_start: 0.8205 (mt) cc_final: 0.7900 (mm) REVERT: L 21 LEU cc_start: 0.8996 (mm) cc_final: 0.8763 (mp) REVERT: L 81 GLU cc_start: 0.8297 (pm20) cc_final: 0.8092 (pm20) REVERT: A 328 ARG cc_start: 0.7702 (tpt90) cc_final: 0.4838 (pmt-80) REVERT: A 420 ASP cc_start: 0.7112 (m-30) cc_final: 0.6345 (t0) REVERT: A 458 LYS cc_start: 0.7823 (pttt) cc_final: 0.6992 (mmtt) REVERT: A 460 ASN cc_start: 0.7098 (m-40) cc_final: 0.6459 (m-40) outliers start: 16 outliers final: 11 residues processed: 89 average time/residue: 0.1569 time to fit residues: 17.1563 Evaluate side-chains 82 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 97 GLN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 398 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 0.0060 chunk 12 optimal weight: 0.0170 chunk 27 optimal weight: 0.0670 chunk 14 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 overall best weight: 0.2372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 97 GLN H 105 GLN L 37 GLN L 100 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.088321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.081103 restraints weight = 9600.615| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.72 r_work: 0.3296 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 3464 Z= 0.168 Angle : 0.635 9.088 4706 Z= 0.325 Chirality : 0.047 0.228 526 Planarity : 0.005 0.048 597 Dihedral : 5.250 24.489 549 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.66 % Allowed : 11.51 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.33 (0.40), residues: 420 helix: -2.23 (1.00), residues: 26 sheet: 0.93 (0.41), residues: 152 loop : -0.75 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 98 HIS 0.001 0.000 HIS L 90 PHE 0.006 0.001 PHE A 497 TYR 0.014 0.002 TYR A 453 ARG 0.005 0.001 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8282 (mt) cc_final: 0.7963 (mm) REVERT: H 110 THR cc_start: 0.8287 (p) cc_final: 0.8049 (p) REVERT: L 12 SER cc_start: 0.8144 (t) cc_final: 0.7844 (m) REVERT: L 21 LEU cc_start: 0.8949 (mm) cc_final: 0.8725 (mp) REVERT: A 328 ARG cc_start: 0.7725 (tpt90) cc_final: 0.4727 (pmt-80) REVERT: A 360 ASN cc_start: 0.9212 (t0) cc_final: 0.8966 (t0) REVERT: A 420 ASP cc_start: 0.7104 (m-30) cc_final: 0.6322 (t0) REVERT: A 458 LYS cc_start: 0.7937 (pttt) cc_final: 0.6989 (mmtt) REVERT: A 460 ASN cc_start: 0.7163 (m-40) cc_final: 0.6547 (m-40) outliers start: 17 outliers final: 11 residues processed: 91 average time/residue: 0.1530 time to fit residues: 17.0420 Evaluate side-chains 83 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 97 GLN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 398 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 97 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.086588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.079454 restraints weight = 9621.260| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.70 r_work: 0.3268 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 3464 Z= 0.264 Angle : 0.636 6.036 4706 Z= 0.333 Chirality : 0.048 0.196 526 Planarity : 0.005 0.044 597 Dihedral : 5.280 26.103 549 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.48 % Allowed : 12.05 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.49 (0.40), residues: 420 helix: -2.23 (1.00), residues: 26 sheet: 0.93 (0.41), residues: 152 loop : -0.97 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 98 HIS 0.001 0.001 HIS L 90 PHE 0.008 0.001 PHE A 486 TYR 0.017 0.002 TYR A 369 ARG 0.004 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8319 (mt) cc_final: 0.8000 (mm) REVERT: H 110 THR cc_start: 0.8264 (p) cc_final: 0.8002 (p) REVERT: L 21 LEU cc_start: 0.8935 (mm) cc_final: 0.8693 (mp) REVERT: A 420 ASP cc_start: 0.7182 (m-30) cc_final: 0.6381 (t0) REVERT: A 458 LYS cc_start: 0.7847 (pttt) cc_final: 0.6961 (mmtt) REVERT: A 460 ASN cc_start: 0.7247 (m-40) cc_final: 0.6614 (m-40) outliers start: 20 outliers final: 14 residues processed: 88 average time/residue: 0.1507 time to fit residues: 16.2920 Evaluate side-chains 84 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 97 GLN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.7980 chunk 6 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 97 GLN H 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.086784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.079482 restraints weight = 9828.496| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.79 r_work: 0.3269 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3464 Z= 0.226 Angle : 0.635 8.445 4706 Z= 0.330 Chirality : 0.048 0.189 526 Planarity : 0.005 0.043 597 Dihedral : 5.169 23.778 549 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.21 % Allowed : 13.42 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.53 (0.40), residues: 420 helix: -2.15 (1.02), residues: 26 sheet: 1.00 (0.42), residues: 152 loop : -1.08 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 98 HIS 0.001 0.001 HIS L 90 PHE 0.010 0.001 PHE A 497 TYR 0.023 0.002 TYR A 453 ARG 0.003 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8331 (mt) cc_final: 0.8025 (mm) REVERT: H 110 THR cc_start: 0.8285 (p) cc_final: 0.8016 (p) REVERT: L 24 ARG cc_start: 0.7364 (mmm-85) cc_final: 0.7102 (mmm-85) REVERT: L 77 ARG cc_start: 0.7667 (mmm-85) cc_final: 0.7166 (tmt170) REVERT: L 81 GLU cc_start: 0.8419 (pm20) cc_final: 0.7925 (pm20) REVERT: A 340 GLU cc_start: 0.8840 (pt0) cc_final: 0.8576 (pt0) REVERT: A 420 ASP cc_start: 0.7203 (m-30) cc_final: 0.6337 (t0) REVERT: A 458 LYS cc_start: 0.7735 (pttt) cc_final: 0.6836 (mmpt) REVERT: A 460 ASN cc_start: 0.7260 (m-40) cc_final: 0.6640 (m-40) outliers start: 19 outliers final: 13 residues processed: 84 average time/residue: 0.1768 time to fit residues: 17.7060 Evaluate side-chains 89 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 97 GLN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 30 optimal weight: 0.0020 chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 97 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.087346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.080155 restraints weight = 9742.937| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.76 r_work: 0.3291 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 3464 Z= 0.188 Angle : 0.620 6.431 4706 Z= 0.321 Chirality : 0.047 0.182 526 Planarity : 0.005 0.043 597 Dihedral : 5.065 24.113 549 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.93 % Allowed : 14.25 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.52 (0.40), residues: 420 helix: -2.26 (0.98), residues: 26 sheet: 1.09 (0.42), residues: 152 loop : -1.13 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 98 HIS 0.001 0.000 HIS L 90 PHE 0.007 0.001 PHE A 497 TYR 0.023 0.002 TYR L 49 ARG 0.002 0.000 ARG L 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8344 (mt) cc_final: 0.8050 (mm) REVERT: H 110 THR cc_start: 0.8246 (p) cc_final: 0.7983 (p) REVERT: L 21 LEU cc_start: 0.8899 (mm) cc_final: 0.8653 (mp) REVERT: L 77 ARG cc_start: 0.7654 (mmm-85) cc_final: 0.7200 (tmt170) REVERT: L 81 GLU cc_start: 0.8332 (pm20) cc_final: 0.8007 (pm20) REVERT: A 340 GLU cc_start: 0.8769 (pt0) cc_final: 0.8492 (pt0) REVERT: A 356 LYS cc_start: 0.8967 (ttpt) cc_final: 0.8692 (ttpt) REVERT: A 360 ASN cc_start: 0.9220 (t0) cc_final: 0.8966 (t0) REVERT: A 420 ASP cc_start: 0.7133 (m-30) cc_final: 0.6266 (t0) REVERT: A 458 LYS cc_start: 0.7618 (pttt) cc_final: 0.6737 (mmpt) REVERT: A 460 ASN cc_start: 0.7246 (m-40) cc_final: 0.6643 (m-40) outliers start: 18 outliers final: 14 residues processed: 87 average time/residue: 0.1714 time to fit residues: 18.2488 Evaluate side-chains 93 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 97 GLN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 97 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.085713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.078541 restraints weight = 9851.697| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.77 r_work: 0.3257 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3464 Z= 0.280 Angle : 0.661 6.235 4706 Z= 0.342 Chirality : 0.047 0.145 526 Planarity : 0.005 0.041 597 Dihedral : 5.140 23.991 549 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.93 % Allowed : 13.42 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.40), residues: 420 helix: -2.20 (0.99), residues: 26 sheet: 1.03 (0.42), residues: 152 loop : -1.32 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 98 HIS 0.001 0.001 HIS L 90 PHE 0.010 0.001 PHE A 329 TYR 0.050 0.002 TYR A 453 ARG 0.004 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: H 110 THR cc_start: 0.8281 (p) cc_final: 0.8001 (p) REVERT: L 21 LEU cc_start: 0.8895 (mm) cc_final: 0.8635 (mp) REVERT: L 77 ARG cc_start: 0.7738 (mmm-85) cc_final: 0.7215 (tmt170) REVERT: L 81 GLU cc_start: 0.8547 (pm20) cc_final: 0.8222 (pm20) REVERT: A 340 GLU cc_start: 0.8833 (pt0) cc_final: 0.8570 (pt0) REVERT: A 356 LYS cc_start: 0.8989 (ttpt) cc_final: 0.8749 (ttmt) REVERT: A 458 LYS cc_start: 0.7684 (pttt) cc_final: 0.6770 (mmpt) REVERT: A 465 GLU cc_start: 0.7140 (tt0) cc_final: 0.6462 (tt0) outliers start: 18 outliers final: 14 residues processed: 83 average time/residue: 0.1668 time to fit residues: 16.7998 Evaluate side-chains 87 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 97 GLN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 0.0000 chunk 15 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 6 optimal weight: 0.5980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 97 GLN H 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.086970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.079701 restraints weight = 9659.042| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.83 r_work: 0.3278 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3464 Z= 0.207 Angle : 0.692 10.168 4706 Z= 0.349 Chirality : 0.047 0.133 526 Planarity : 0.005 0.041 597 Dihedral : 5.315 25.067 549 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.84 % Allowed : 15.07 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.40), residues: 420 helix: -2.31 (1.00), residues: 26 sheet: 1.15 (0.42), residues: 152 loop : -1.33 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 98 HIS 0.001 0.000 HIS L 90 PHE 0.005 0.001 PHE A 497 TYR 0.023 0.002 TYR L 49 ARG 0.002 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 THR cc_start: 0.8239 (p) cc_final: 0.7950 (p) REVERT: L 21 LEU cc_start: 0.8881 (mm) cc_final: 0.8629 (mp) REVERT: L 77 ARG cc_start: 0.7704 (mmm-85) cc_final: 0.6952 (tmt170) REVERT: L 81 GLU cc_start: 0.8577 (pm20) cc_final: 0.8281 (pm20) REVERT: A 340 GLU cc_start: 0.8853 (pt0) cc_final: 0.8584 (pt0) REVERT: A 360 ASN cc_start: 0.9242 (t0) cc_final: 0.8979 (t0) REVERT: A 458 LYS cc_start: 0.7647 (pttt) cc_final: 0.6703 (mmpt) REVERT: A 465 GLU cc_start: 0.7138 (tt0) cc_final: 0.6412 (tt0) outliers start: 14 outliers final: 12 residues processed: 89 average time/residue: 0.1636 time to fit residues: 17.5298 Evaluate side-chains 89 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 97 GLN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.084641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.077560 restraints weight = 9779.520| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.71 r_work: 0.3230 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 3464 Z= 0.339 Angle : 0.721 9.039 4706 Z= 0.376 Chirality : 0.050 0.200 526 Planarity : 0.006 0.039 597 Dihedral : 5.378 24.380 549 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.56 % Allowed : 16.16 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.80 (0.41), residues: 420 helix: -2.36 (0.97), residues: 26 sheet: 1.05 (0.42), residues: 153 loop : -1.47 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 47 HIS 0.002 0.001 HIS L 90 PHE 0.013 0.002 PHE A 486 TYR 0.059 0.003 TYR A 453 ARG 0.006 0.001 ARG A 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 21 LEU cc_start: 0.8888 (mm) cc_final: 0.8605 (mp) REVERT: L 77 ARG cc_start: 0.7733 (mmm-85) cc_final: 0.7182 (tmt170) REVERT: A 340 GLU cc_start: 0.8859 (pt0) cc_final: 0.8606 (pt0) REVERT: A 356 LYS cc_start: 0.9029 (ttpt) cc_final: 0.8821 (ttmt) REVERT: A 360 ASN cc_start: 0.9237 (t0) cc_final: 0.8960 (t0) REVERT: A 458 LYS cc_start: 0.7625 (pttt) cc_final: 0.6711 (mmpt) outliers start: 13 outliers final: 12 residues processed: 80 average time/residue: 0.1717 time to fit residues: 16.5849 Evaluate side-chains 87 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 97 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.086088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.078972 restraints weight = 9735.483| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.76 r_work: 0.3260 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3464 Z= 0.229 Angle : 0.681 8.334 4706 Z= 0.350 Chirality : 0.048 0.173 526 Planarity : 0.005 0.039 597 Dihedral : 5.248 26.441 549 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.01 % Allowed : 17.26 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.80 (0.41), residues: 420 helix: -2.40 (0.97), residues: 26 sheet: 1.12 (0.43), residues: 152 loop : -1.51 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS A 519 PHE 0.007 0.001 PHE A 329 TYR 0.019 0.002 TYR A 453 ARG 0.005 0.001 ARG L 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2188.59 seconds wall clock time: 39 minutes 29.08 seconds (2369.08 seconds total)