Starting phenix.real_space_refine on Wed Mar 5 20:39:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ru4_24696/03_2025/7ru4_24696.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ru4_24696/03_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_24696/03_2025/7ru4_24696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ru4_24696/03_2025/7ru4_24696.map" model { file = "/net/cci-nas-00/data/ceres_data/7ru4_24696/03_2025/7ru4_24696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ru4_24696/03_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-5624/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: 3.56, per 1000 atoms: 1.05 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: 0.87 Conformation dependent library (CDL) restraints added in 378.9 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: 0.46 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: 0.93 Time building geometry restraints manager: 1.04 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: 4.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.840 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.540 ------------------------------------------------------------------------------- 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 : 0.333 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: 0.2428 time to fit residues: 33.7463 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 : 0.402 ------------------------------------------------------------------------------- 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: 0.6980 chunk 37 optimal weight: 0.7980 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 = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.081004 restraints weight = 9493.794| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.69 r_work: 0.3312 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- 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 10.124 4706 Z= 0.392 Chirality : 0.050 0.184 526 Planarity : 0.005 0.041 597 Dihedral : 5.821 25.560 549 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 : 0.404 Fit side-chains REVERT: H 100 LEU cc_start: 0.9361 (mt) cc_final: 0.9085 (mt) REVERT: L 21 LEU cc_start: 0.8974 (mm) cc_final: 0.8736 (mp) REVERT: A 328 ARG cc_start: 0.7625 (tpt90) cc_final: 0.4681 (pmt-80) REVERT: A 356 LYS cc_start: 0.8807 (tttt) cc_final: 0.7994 (tttt) REVERT: A 420 ASP cc_start: 0.6853 (m-30) cc_final: 0.6070 (t0) REVERT: A 458 LYS cc_start: 0.7876 (pttt) cc_final: 0.7036 (mmpt) REVERT: A 460 ASN cc_start: 0.6993 (m-40) cc_final: 0.6322 (m-40) outliers start: 15 outliers final: 7 residues processed: 100 average time/residue: 0.1665 time to fit residues: 20.0154 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 : 0.402 ------------------------------------------------------------------------------- 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: 1.9990 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 A 501 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.082633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.075524 restraints weight = 9487.970| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.69 r_work: 0.3208 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 3464 Z= 0.466 Angle : 0.799 8.081 4706 Z= 0.424 Chirality : 0.051 0.207 526 Planarity : 0.006 0.045 597 Dihedral : 6.562 48.826 549 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.93 % Allowed : 11.51 % Favored : 83.56 % 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: -2.05 (1.08), residues: 25 sheet: 0.66 (0.41), residues: 150 loop : -1.04 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 103 HIS 0.003 0.002 HIS L 90 PHE 0.020 0.003 PHE A 486 TYR 0.021 0.003 TYR A 369 ARG 0.008 0.001 ARG A 454 *********************** 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 93 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.402 Fit side-chains REVERT: L 21 LEU cc_start: 0.8990 (mm) cc_final: 0.8715 (mp) REVERT: L 49 TYR cc_start: 0.9303 (p90) cc_final: 0.9009 (p90) REVERT: L 77 ARG cc_start: 0.7850 (mmm-85) cc_final: 0.7142 (tmt170) REVERT: A 392 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7518 (m-80) REVERT: A 420 ASP cc_start: 0.7022 (m-30) cc_final: 0.6128 (t0) REVERT: A 458 LYS cc_start: 0.7781 (pttt) cc_final: 0.7025 (mmpt) REVERT: A 460 ASN cc_start: 0.7161 (m-40) cc_final: 0.6388 (m-40) REVERT: A 525 CYS cc_start: 0.6348 (m) cc_final: 0.6120 (m) outliers start: 18 outliers final: 12 residues processed: 84 average time/residue: 0.1648 time to fit residues: 16.7559 Evaluate side-chains 82 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 28 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 0.0170 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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 100 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.083476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.075800 restraints weight = 9767.775| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.96 r_work: 0.3200 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3464 Z= 0.231 Angle : 0.663 7.802 4706 Z= 0.344 Chirality : 0.048 0.209 526 Planarity : 0.005 0.049 597 Dihedral : 5.913 34.282 549 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.93 % Allowed : 12.60 % 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: -0.68 (0.40), residues: 420 helix: -2.21 (1.00), residues: 26 sheet: 0.79 (0.41), residues: 152 loop : -1.11 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 103 HIS 0.001 0.001 HIS A 519 PHE 0.011 0.001 PHE L 83 TYR 0.018 0.002 TYR A 369 ARG 0.003 0.001 ARG A 346 *********************** 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: 18 poor density : 82 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 85 GLU cc_start: 0.8783 (mp0) cc_final: 0.8519 (mp0) REVERT: L 21 LEU cc_start: 0.8939 (mm) cc_final: 0.8689 (mp) REVERT: L 49 TYR cc_start: 0.9166 (p90) cc_final: 0.8955 (p90) REVERT: L 77 ARG cc_start: 0.7850 (mmm-85) cc_final: 0.6993 (tmt170) REVERT: A 360 ASN cc_start: 0.9212 (t0) cc_final: 0.8964 (t0) REVERT: A 389 ASP cc_start: 0.8129 (m-30) cc_final: 0.7880 (m-30) REVERT: A 392 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7173 (m-80) REVERT: A 420 ASP cc_start: 0.7345 (m-30) cc_final: 0.6408 (t0) REVERT: A 458 LYS cc_start: 0.7766 (pttt) cc_final: 0.6828 (mmpt) REVERT: A 460 ASN cc_start: 0.7254 (m-40) cc_final: 0.6540 (m-40) outliers start: 18 outliers final: 10 residues processed: 89 average time/residue: 0.1683 time to fit residues: 18.4971 Evaluate side-chains 85 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 100 GLN 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 503 VAL 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: 0.8980 chunk 29 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 0 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 16 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.083660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.076022 restraints weight = 9704.647| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.94 r_work: 0.3202 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3464 Z= 0.227 Angle : 0.627 6.173 4706 Z= 0.325 Chirality : 0.047 0.192 526 Planarity : 0.005 0.045 597 Dihedral : 5.928 41.691 549 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.21 % Allowed : 12.88 % Favored : 81.92 % 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: -2.34 (0.97), residues: 26 sheet: 0.90 (0.41), residues: 152 loop : -1.20 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 98 HIS 0.001 0.001 HIS L 90 PHE 0.009 0.001 PHE A 497 TYR 0.019 0.002 TYR A 453 ARG 0.003 0.000 ARG A 346 *********************** 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 99 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 110 THR cc_start: 0.8227 (p) cc_final: 0.7922 (p) REVERT: L 21 LEU cc_start: 0.8930 (mm) cc_final: 0.8674 (mp) REVERT: L 77 ARG cc_start: 0.7884 (mmm-85) cc_final: 0.7097 (tmt170) REVERT: L 81 GLU cc_start: 0.8548 (pm20) cc_final: 0.8080 (pm20) REVERT: A 360 ASN cc_start: 0.9213 (t0) cc_final: 0.8981 (t0) REVERT: A 389 ASP cc_start: 0.8185 (m-30) cc_final: 0.7948 (m-30) REVERT: A 392 PHE cc_start: 0.7887 (OUTLIER) cc_final: 0.7068 (m-80) REVERT: A 420 ASP cc_start: 0.7389 (m-30) cc_final: 0.6487 (t0) REVERT: A 453 TYR cc_start: 0.5342 (m-80) cc_final: 0.5136 (m-80) REVERT: A 458 LYS cc_start: 0.7742 (pttt) cc_final: 0.6774 (mmpt) REVERT: A 460 ASN cc_start: 0.7300 (m-40) cc_final: 0.6588 (m-40) outliers start: 19 outliers final: 13 residues processed: 88 average time/residue: 0.1659 time to fit residues: 17.6516 Evaluate side-chains 91 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 33 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 100 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.0010 chunk 6 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 40 optimal weight: 0.0370 overall best weight: 0.2464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.084939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.077290 restraints weight = 9867.476| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.99 r_work: 0.3227 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3464 Z= 0.160 Angle : 0.628 9.903 4706 Z= 0.320 Chirality : 0.048 0.217 526 Planarity : 0.005 0.045 597 Dihedral : 5.582 30.425 549 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.38 % Allowed : 14.52 % 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: -0.59 (0.41), residues: 420 helix: -2.26 (1.01), residues: 26 sheet: 1.02 (0.42), residues: 152 loop : -1.16 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 98 HIS 0.000 0.000 HIS L 90 PHE 0.008 0.001 PHE A 497 TYR 0.014 0.001 TYR A 495 ARG 0.002 0.000 ARG L 61 *********************** 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 98 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.8639 (pm20) cc_final: 0.8406 (pm20) REVERT: H 110 THR cc_start: 0.8187 (p) cc_final: 0.7870 (p) REVERT: L 21 LEU cc_start: 0.8913 (mm) cc_final: 0.8669 (mp) REVERT: L 77 ARG cc_start: 0.7841 (mmm-85) cc_final: 0.7047 (tmt170) REVERT: L 81 GLU cc_start: 0.8510 (pm20) cc_final: 0.8191 (pm20) REVERT: A 389 ASP cc_start: 0.8171 (m-30) cc_final: 0.7959 (m-30) REVERT: A 392 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7079 (m-80) REVERT: A 420 ASP cc_start: 0.7415 (m-30) cc_final: 0.6487 (t0) REVERT: A 458 LYS cc_start: 0.7730 (pttt) cc_final: 0.6770 (mmpt) REVERT: A 460 ASN cc_start: 0.7276 (m-40) cc_final: 0.6595 (m-40) outliers start: 16 outliers final: 11 residues processed: 87 average time/residue: 0.1713 time to fit residues: 18.0001 Evaluate side-chains 88 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 100 GLN 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 402 ILE 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: 0.0980 chunk 21 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 0.0970 chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 6 optimal weight: 0.0470 chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 overall best weight: 0.2276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 105 GLN A 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.085827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.078072 restraints weight = 9865.089| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.99 r_work: 0.3244 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3464 Z= 0.166 Angle : 0.625 7.325 4706 Z= 0.318 Chirality : 0.047 0.173 526 Planarity : 0.005 0.042 597 Dihedral : 5.519 36.762 549 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.38 % Allowed : 15.89 % 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: -0.57 (0.40), residues: 420 helix: -2.37 (0.96), residues: 26 sheet: 1.01 (0.42), residues: 152 loop : -1.11 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 98 HIS 0.000 0.000 HIS L 90 PHE 0.009 0.001 PHE A 497 TYR 0.027 0.002 TYR A 453 ARG 0.002 0.000 ARG L 61 *********************** 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 97 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 THR cc_start: 0.8169 (p) cc_final: 0.7868 (p) REVERT: L 21 LEU cc_start: 0.8915 (mm) cc_final: 0.8655 (mp) REVERT: L 77 ARG cc_start: 0.7859 (mmm-85) cc_final: 0.7050 (tmt170) REVERT: L 81 GLU cc_start: 0.8524 (pm20) cc_final: 0.8272 (pm20) REVERT: A 340 GLU cc_start: 0.8756 (pt0) cc_final: 0.8011 (pp20) REVERT: A 386 LYS cc_start: 0.4371 (mttt) cc_final: 0.2890 (mtpt) REVERT: A 389 ASP cc_start: 0.8151 (m-30) cc_final: 0.7935 (m-30) REVERT: A 392 PHE cc_start: 0.7739 (OUTLIER) cc_final: 0.7207 (m-80) REVERT: A 420 ASP cc_start: 0.7448 (m-30) cc_final: 0.6522 (t0) REVERT: A 458 LYS cc_start: 0.7739 (pttt) cc_final: 0.6757 (mmpt) REVERT: A 460 ASN cc_start: 0.7277 (m-40) cc_final: 0.6620 (m-40) outliers start: 16 outliers final: 10 residues processed: 86 average time/residue: 0.1713 time to fit residues: 17.6766 Evaluate side-chains 86 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 100 GLN Chi-restraints excluded: chain A residue 332 ILE 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 402 ILE 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: 1.9990 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 30 optimal weight: 0.0970 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.084679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.077089 restraints weight = 9874.459| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.93 r_work: 0.3222 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3464 Z= 0.217 Angle : 0.638 6.117 4706 Z= 0.329 Chirality : 0.046 0.135 526 Planarity : 0.005 0.039 597 Dihedral : 5.641 42.033 549 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.47 % Allowed : 17.26 % 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: -0.56 (0.40), residues: 420 helix: -2.36 (0.95), residues: 26 sheet: 1.05 (0.43), residues: 152 loop : -1.14 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 98 HIS 0.001 0.000 HIS L 90 PHE 0.009 0.001 PHE L 71 TYR 0.026 0.002 TYR L 49 ARG 0.003 0.001 ARG A 346 *********************** 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 87 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 THR cc_start: 0.8249 (p) cc_final: 0.7937 (p) REVERT: L 21 LEU cc_start: 0.8937 (mm) cc_final: 0.8669 (mp) REVERT: L 77 ARG cc_start: 0.7893 (mmm-85) cc_final: 0.7076 (tmt170) REVERT: L 81 GLU cc_start: 0.8602 (pm20) cc_final: 0.8358 (pm20) REVERT: A 340 GLU cc_start: 0.8830 (pt0) cc_final: 0.8130 (pp20) REVERT: A 378 LYS cc_start: 0.8728 (mmmm) cc_final: 0.8360 (mmmt) REVERT: A 386 LYS cc_start: 0.4423 (mttt) cc_final: 0.2901 (mtpt) REVERT: A 389 ASP cc_start: 0.8182 (m-30) cc_final: 0.7976 (m-30) REVERT: A 392 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.7188 (m-80) REVERT: A 420 ASP cc_start: 0.7452 (m-30) cc_final: 0.6546 (t0) REVERT: A 458 LYS cc_start: 0.7557 (pttt) cc_final: 0.6609 (mmpt) REVERT: A 460 ASN cc_start: 0.7340 (m-40) cc_final: 0.6686 (m-40) outliers start: 9 outliers final: 8 residues processed: 80 average time/residue: 0.1525 time to fit residues: 14.9897 Evaluate side-chains 86 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 A residue 332 ILE 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 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 0.0370 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.084872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.077323 restraints weight = 9674.499| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.90 r_work: 0.3228 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3464 Z= 0.206 Angle : 0.639 6.742 4706 Z= 0.330 Chirality : 0.047 0.149 526 Planarity : 0.005 0.038 597 Dihedral : 5.687 47.437 549 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % 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: -0.63 (0.40), residues: 420 helix: -2.41 (0.94), residues: 26 sheet: 1.03 (0.43), residues: 152 loop : -1.20 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 98 HIS 0.002 0.001 HIS A 519 PHE 0.009 0.001 PHE A 497 TYR 0.026 0.002 TYR L 49 ARG 0.004 0.001 ARG L 24 *********************** 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 88 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 PHE cc_start: 0.8740 (m-80) cc_final: 0.8528 (m-10) REVERT: L 21 LEU cc_start: 0.8911 (mm) cc_final: 0.8637 (mp) REVERT: L 77 ARG cc_start: 0.7908 (mmm-85) cc_final: 0.7132 (tmt170) REVERT: A 340 GLU cc_start: 0.8813 (pt0) cc_final: 0.8144 (pp20) REVERT: A 378 LYS cc_start: 0.8723 (mmmm) cc_final: 0.8389 (mmmt) REVERT: A 386 LYS cc_start: 0.4295 (mttt) cc_final: 0.2845 (mtpt) REVERT: A 392 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.7191 (m-80) REVERT: A 458 LYS cc_start: 0.7545 (pttt) cc_final: 0.6612 (mmpt) outliers start: 11 outliers final: 8 residues processed: 81 average time/residue: 0.1489 time to fit residues: 14.8892 Evaluate side-chains 83 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 332 ILE 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 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: 1.9990 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 = 0.3440 r_free = 0.3440 target = 0.083925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.076379 restraints weight = 9812.458| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.91 r_work: 0.3207 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3464 Z= 0.255 Angle : 0.718 11.833 4706 Z= 0.367 Chirality : 0.049 0.166 526 Planarity : 0.005 0.039 597 Dihedral : 6.207 46.143 549 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.74 % Allowed : 17.81 % Favored : 79.45 % 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: -0.75 (0.41), residues: 420 helix: -2.56 (0.94), residues: 26 sheet: 1.04 (0.43), residues: 152 loop : -1.35 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 98 HIS 0.002 0.001 HIS L 90 PHE 0.010 0.001 PHE L 71 TYR 0.026 0.002 TYR L 49 ARG 0.004 0.001 ARG L 24 ********************** 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 87 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 PHE cc_start: 0.8748 (m-80) cc_final: 0.8532 (m-10) REVERT: L 21 LEU cc_start: 0.8913 (mm) cc_final: 0.8615 (mp) REVERT: L 77 ARG cc_start: 0.7896 (mmm-85) cc_final: 0.7050 (tmt170) REVERT: L 81 GLU cc_start: 0.8534 (pm20) cc_final: 0.8005 (pm20) REVERT: A 340 GLU cc_start: 0.8832 (pt0) cc_final: 0.8170 (pp20) REVERT: A 378 LYS cc_start: 0.8760 (mmmm) cc_final: 0.8400 (mmmt) REVERT: A 386 LYS cc_start: 0.4332 (mttt) cc_final: 0.2841 (mtpt) REVERT: A 392 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.7135 (m-80) REVERT: A 458 LYS cc_start: 0.7563 (pttt) cc_final: 0.6598 (mmpt) outliers start: 10 outliers final: 8 residues processed: 80 average time/residue: 0.1450 time to fit residues: 14.2915 Evaluate side-chains 84 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 332 ILE 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 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: 2.9990 chunk 23 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.083718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.076109 restraints weight = 9778.835| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.92 r_work: 0.3201 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.5515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3464 Z= 0.247 Angle : 0.711 11.912 4706 Z= 0.363 Chirality : 0.048 0.164 526 Planarity : 0.005 0.038 597 Dihedral : 5.993 40.294 549 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.01 % Allowed : 18.08 % Favored : 78.90 % 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: -0.82 (0.41), residues: 420 helix: -2.55 (0.94), residues: 26 sheet: 1.06 (0.43), residues: 150 loop : -1.44 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 98 HIS 0.002 0.001 HIS A 519 PHE 0.008 0.001 PHE A 486 TYR 0.049 0.002 TYR A 453 ARG 0.004 0.001 ARG L 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2191.36 seconds wall clock time: 38 minutes 17.25 seconds (2297.25 seconds total)