Starting phenix.real_space_refine on Wed Mar 5 19:45:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f63_31471/03_2025/7f63_31471.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f63_31471/03_2025/7f63_31471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f63_31471/03_2025/7f63_31471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f63_31471/03_2025/7f63_31471.map" model { file = "/net/cci-nas-00/data/ceres_data/7f63_31471/03_2025/7f63_31471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f63_31471/03_2025/7f63_31471.cif" } resolution = 3.9 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= -0.000 sd= 0.031 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 15 5.16 5 C 2149 2.51 5 N 555 2.21 5 O 656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 3375 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1578 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 187} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 945 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 852 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Time building chain proxies: 3.40, per 1000 atoms: 1.01 Number of scatterers: 3375 At special positions: 0 Unit cell: (67.1, 80.3, 115.5, 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 15 16.00 O 656 8.00 N 555 7.00 C 2149 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 401.6 milliseconds 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 790 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 7 sheets defined 8.6% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.402A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 4.479A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.599A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.721A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 5.509A 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 439 through 442 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 5.006A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.127A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS H 23 " --> pdb=" O GLN H 5 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.760A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.750A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 19 through 22 removed outlier: 4.198A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) 82 hydrogen bonds defined for protein. 192 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: 0.77 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1061 1.34 - 1.46: 912 1.46 - 1.58: 1472 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 3463 Sorted by residual: bond pdb=" C ALA A 520 " pdb=" N PRO A 521 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.23e-01 bond pdb=" CA ASN A 394 " pdb=" CB ASN A 394 " ideal model delta sigma weight residual 1.527 1.542 -0.015 1.61e-02 3.86e+03 8.66e-01 bond pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 1.808 1.779 0.029 3.30e-02 9.18e+02 7.56e-01 bond pdb=" N ASN A 394 " pdb=" CA ASN A 394 " ideal model delta sigma weight residual 1.460 1.472 -0.012 1.42e-02 4.96e+03 7.05e-01 bond pdb=" CA ILE L 75 " pdb=" C ILE L 75 " ideal model delta sigma weight residual 1.523 1.532 -0.009 1.16e-02 7.43e+03 6.11e-01 ... (remaining 3458 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 4612 1.66 - 3.33: 71 3.33 - 4.99: 16 4.99 - 6.65: 3 6.65 - 8.31: 2 Bond angle restraints: 4704 Sorted by residual: angle pdb=" C LEU H 70 " pdb=" N THR H 71 " pdb=" CA THR H 71 " ideal model delta sigma weight residual 121.75 117.03 4.72 1.73e+00 3.34e-01 7.43e+00 angle pdb=" C TYR H 80 " pdb=" N MET H 81 " pdb=" CA MET H 81 " ideal model delta sigma weight residual 122.65 126.43 -3.78 1.49e+00 4.50e-01 6.45e+00 angle pdb=" C THR A 393 " pdb=" N ASN A 394 " pdb=" CA ASN A 394 " ideal model delta sigma weight residual 122.82 126.21 -3.39 1.42e+00 4.96e-01 5.72e+00 angle pdb=" CA LEU H 70 " pdb=" CB LEU H 70 " pdb=" CG LEU H 70 " ideal model delta sigma weight residual 116.30 124.61 -8.31 3.50e+00 8.16e-02 5.64e+00 angle pdb=" C ASN A 331 " pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 121.97 125.97 -4.00 1.80e+00 3.09e-01 4.94e+00 ... (remaining 4699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 1824 16.04 - 32.08: 153 32.08 - 48.12: 47 48.12 - 64.15: 8 64.15 - 80.19: 4 Dihedral angle restraints: 2036 sinusoidal: 788 harmonic: 1248 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 12.81 80.19 1 1.00e+01 1.00e-02 7.96e+01 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 93.00 154.13 -61.13 1 1.00e+01 1.00e-02 4.96e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual -86.00 -46.16 -39.84 1 1.00e+01 1.00e-02 2.23e+01 ... (remaining 2033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 304 0.032 - 0.064: 132 0.064 - 0.096: 37 0.096 - 0.128: 23 0.128 - 0.160: 5 Chirality restraints: 501 Sorted by residual: chirality pdb=" CB ILE A 332 " pdb=" CA ILE A 332 " pdb=" CG1 ILE A 332 " pdb=" CG2 ILE A 332 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" CG LEU H 70 " pdb=" CB LEU H 70 " pdb=" CD1 LEU H 70 " pdb=" CD2 LEU H 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ASN A 394 " pdb=" N ASN A 394 " pdb=" C ASN A 394 " pdb=" CB ASN A 394 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 498 not shown) Planarity restraints: 605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 64 " 0.014 2.00e-02 2.50e+03 2.31e-02 9.32e+00 pdb=" CG PHE H 64 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE H 64 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE H 64 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE H 64 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE H 64 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE H 64 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 336 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO A 337 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 29 " 0.006 2.00e-02 2.50e+03 8.93e-03 1.40e+00 pdb=" CG PHE H 29 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE H 29 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE H 29 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE H 29 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE H 29 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE H 29 " -0.000 2.00e-02 2.50e+03 ... (remaining 602 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 92 2.69 - 3.24: 3188 3.24 - 3.79: 5100 3.79 - 4.35: 6634 4.35 - 4.90: 10708 Nonbonded interactions: 25722 Sorted by model distance: nonbonded pdb=" O HIS L 61 " pdb=" OG SER L 76 " model vdw 2.136 3.040 nonbonded pdb=" O ALA H 106 " pdb=" OH TYR L 36 " model vdw 2.141 3.040 nonbonded pdb=" OG1 THR H 28 " pdb=" OE2 GLU H 31 " model vdw 2.170 3.040 nonbonded pdb=" O CYS H 22 " pdb=" OG1 THR H 78 " model vdw 2.290 3.040 nonbonded pdb=" NH2 ARG A 346 " pdb=" OH TYR A 451 " model vdw 2.330 3.120 ... (remaining 25717 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 group one per residue 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: 3.700 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.330 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6102 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 : 0.002 0.029 3463 Z= 0.130 Angle : 0.575 8.312 4704 Z= 0.299 Chirality : 0.044 0.160 501 Planarity : 0.004 0.047 605 Dihedral : 13.336 74.505 1228 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.31 % Favored : 91.45 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.39), residues: 421 helix: -3.88 (0.95), residues: 12 sheet: 0.31 (0.48), residues: 132 loop : -2.56 (0.33), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 36 HIS 0.000 0.000 HIS A 519 PHE 0.052 0.002 PHE H 64 TYR 0.016 0.001 TYR L 49 ARG 0.002 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.7649 (m-30) cc_final: 0.6909 (m-30) REVERT: A 406 GLU cc_start: 0.8120 (mp0) cc_final: 0.7712 (mp0) REVERT: H 101 TYR cc_start: 0.6569 (t80) cc_final: 0.6301 (t80) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2150 time to fit residues: 29.0182 Evaluate side-chains 67 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 0.2980 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 0.2980 chunk 11 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.118951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.108347 restraints weight = 11744.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.110261 restraints weight = 7572.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.111578 restraints weight = 5331.769| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3463 Z= 0.193 Angle : 0.710 11.196 4704 Z= 0.366 Chirality : 0.047 0.206 501 Planarity : 0.004 0.036 605 Dihedral : 4.847 25.931 472 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.74 % Favored : 89.79 % Rotamer: Outliers : 1.89 % Allowed : 13.21 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.34 (0.39), residues: 421 helix: -2.95 (0.99), residues: 20 sheet: 0.33 (0.48), residues: 131 loop : -2.61 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 35 HIS 0.002 0.001 HIS L 61 PHE 0.023 0.002 PHE H 29 TYR 0.012 0.001 TYR L 53 ARG 0.005 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLN cc_start: 0.8071 (mp10) cc_final: 0.7718 (mp10) outliers start: 7 outliers final: 2 residues processed: 86 average time/residue: 0.1716 time to fit residues: 17.6385 Evaluate side-chains 63 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 443 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN H 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.111536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.100571 restraints weight = 11342.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.102433 restraints weight = 7372.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.103683 restraints weight = 5243.246| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3463 Z= 0.203 Angle : 0.698 11.421 4704 Z= 0.369 Chirality : 0.048 0.213 501 Planarity : 0.004 0.036 605 Dihedral : 5.232 17.577 472 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.69 % Favored : 88.84 % Rotamer: Outliers : 3.50 % Allowed : 17.25 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.40), residues: 421 helix: -3.14 (0.93), residues: 20 sheet: 0.21 (0.49), residues: 136 loop : -2.55 (0.34), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 36 HIS 0.003 0.001 HIS L 61 PHE 0.018 0.002 PHE H 29 TYR 0.014 0.002 TYR H 103 ARG 0.006 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8157 (tmt-80) cc_final: 0.7916 (tpt90) REVERT: H 33 THR cc_start: 0.9256 (OUTLIER) cc_final: 0.8948 (t) REVERT: H 62 GLN cc_start: 0.7444 (tm-30) cc_final: 0.7107 (tm-30) REVERT: L 83 LEU cc_start: 0.6889 (tt) cc_final: 0.6580 (pp) REVERT: L 91 TYR cc_start: 0.8513 (p90) cc_final: 0.8013 (p90) outliers start: 13 outliers final: 10 residues processed: 83 average time/residue: 0.1984 time to fit residues: 19.3236 Evaluate side-chains 69 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 55 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 20 optimal weight: 0.0270 chunk 29 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 0.0030 chunk 8 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.4848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 112 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 = 0.4033 r_free = 0.4033 target = 0.112775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.101945 restraints weight = 11549.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.103841 restraints weight = 7432.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.105133 restraints weight = 5326.940| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3463 Z= 0.185 Angle : 0.694 11.609 4704 Z= 0.361 Chirality : 0.047 0.213 501 Planarity : 0.004 0.038 605 Dihedral : 5.245 18.913 472 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.79 % Favored : 90.74 % Rotamer: Outliers : 1.08 % Allowed : 21.02 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.40), residues: 421 helix: -3.27 (0.84), residues: 20 sheet: 0.19 (0.50), residues: 133 loop : -2.48 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 36 HIS 0.003 0.001 HIS L 61 PHE 0.017 0.001 PHE H 29 TYR 0.014 0.001 TYR H 60 ARG 0.004 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8020 (tmt-80) cc_final: 0.7738 (tpt90) REVERT: H 62 GLN cc_start: 0.7393 (tm-30) cc_final: 0.7162 (tm-30) REVERT: L 85 GLU cc_start: 0.7265 (tm-30) cc_final: 0.5850 (tm-30) REVERT: L 87 PHE cc_start: 0.6103 (m-80) cc_final: 0.5724 (m-10) REVERT: L 91 TYR cc_start: 0.8549 (p90) cc_final: 0.8130 (p90) outliers start: 4 outliers final: 3 residues processed: 69 average time/residue: 0.1780 time to fit residues: 14.6402 Evaluate side-chains 59 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain L residue 15 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 0.0670 chunk 22 optimal weight: 0.4980 chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** A 493 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 = 0.4004 r_free = 0.4004 target = 0.111142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.100469 restraints weight = 11555.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.102319 restraints weight = 7333.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.103582 restraints weight = 5175.516| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.5798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3463 Z= 0.199 Angle : 0.696 11.093 4704 Z= 0.365 Chirality : 0.047 0.192 501 Planarity : 0.005 0.067 605 Dihedral : 5.295 19.552 472 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.98 % Favored : 89.55 % Rotamer: Outliers : 3.77 % Allowed : 19.95 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.40), residues: 421 helix: -3.13 (0.74), residues: 26 sheet: 0.20 (0.50), residues: 133 loop : -2.56 (0.35), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 36 HIS 0.001 0.000 HIS L 61 PHE 0.022 0.002 PHE H 63 TYR 0.014 0.001 TYR H 80 ARG 0.003 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 83 LEU cc_start: 0.6725 (tt) cc_final: 0.6382 (pp) outliers start: 14 outliers final: 7 residues processed: 75 average time/residue: 0.1522 time to fit residues: 14.0982 Evaluate side-chains 62 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 55 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.108671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.098111 restraints weight = 11826.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.099876 restraints weight = 7535.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.101094 restraints weight = 5334.674| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.6505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3463 Z= 0.265 Angle : 0.765 11.778 4704 Z= 0.404 Chirality : 0.049 0.216 501 Planarity : 0.005 0.065 605 Dihedral : 5.758 23.194 472 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.48 % Allowed : 13.06 % Favored : 86.46 % Rotamer: Outliers : 3.77 % Allowed : 20.22 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.39), residues: 421 helix: -3.84 (0.54), residues: 26 sheet: -0.05 (0.49), residues: 134 loop : -2.69 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 36 HIS 0.003 0.001 HIS L 61 PHE 0.014 0.002 PHE H 109 TYR 0.039 0.002 TYR L 91 ARG 0.003 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8037 (tmt-80) cc_final: 0.7575 (tpt90) REVERT: A 498 GLN cc_start: 0.7968 (mp10) cc_final: 0.7389 (mp10) REVERT: L 55 TYR cc_start: 0.3622 (OUTLIER) cc_final: 0.1839 (m-10) REVERT: L 83 LEU cc_start: 0.7080 (tt) cc_final: 0.6632 (pp) outliers start: 14 outliers final: 6 residues processed: 72 average time/residue: 0.1621 time to fit residues: 14.4076 Evaluate side-chains 64 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 11 optimal weight: 0.0040 chunk 2 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 1 optimal weight: 0.7980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 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 = 0.3994 r_free = 0.3994 target = 0.110754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.100577 restraints weight = 11578.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.102429 restraints weight = 7184.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.103691 restraints weight = 4970.642| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.6619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3463 Z= 0.216 Angle : 0.747 11.837 4704 Z= 0.390 Chirality : 0.048 0.226 501 Planarity : 0.005 0.049 605 Dihedral : 5.664 23.046 472 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.21 % Favored : 89.31 % Rotamer: Outliers : 2.16 % Allowed : 23.18 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.39), residues: 421 helix: -4.09 (0.54), residues: 26 sheet: -0.08 (0.49), residues: 132 loop : -2.76 (0.34), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 35 HIS 0.003 0.001 HIS L 61 PHE 0.049 0.002 PHE H 64 TYR 0.023 0.001 TYR L 91 ARG 0.002 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLN cc_start: 0.7992 (mp10) cc_final: 0.7441 (mp10) REVERT: L 83 LEU cc_start: 0.7019 (tt) cc_final: 0.6576 (pp) outliers start: 8 outliers final: 6 residues processed: 69 average time/residue: 0.1375 time to fit residues: 11.8902 Evaluate side-chains 61 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 55 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 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 = 0.3993 r_free = 0.3993 target = 0.110667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.100633 restraints weight = 11353.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.102362 restraints weight = 7207.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.103560 restraints weight = 5080.419| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.6834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3463 Z= 0.222 Angle : 0.782 12.416 4704 Z= 0.408 Chirality : 0.049 0.219 501 Planarity : 0.005 0.048 605 Dihedral : 5.494 20.520 472 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.88 % Favored : 87.65 % Rotamer: Outliers : 2.43 % Allowed : 23.45 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.39), residues: 421 helix: -4.14 (0.56), residues: 26 sheet: -0.21 (0.47), residues: 135 loop : -2.75 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 36 HIS 0.004 0.001 HIS L 61 PHE 0.018 0.001 PHE H 109 TYR 0.022 0.001 TYR L 91 ARG 0.003 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLN cc_start: 0.8006 (mp10) cc_final: 0.7476 (mp10) REVERT: L 24 LYS cc_start: 0.3380 (OUTLIER) cc_final: 0.2300 (tmtt) REVERT: L 79 GLN cc_start: 0.1971 (OUTLIER) cc_final: 0.1737 (mm-40) REVERT: L 83 LEU cc_start: 0.6741 (tt) cc_final: 0.6362 (pp) outliers start: 9 outliers final: 6 residues processed: 66 average time/residue: 0.1602 time to fit residues: 12.8621 Evaluate side-chains 63 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 14 optimal weight: 0.0670 chunk 34 optimal weight: 0.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 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 = 0.3981 r_free = 0.3981 target = 0.110082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.099998 restraints weight = 11371.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.101679 restraints weight = 7260.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.102873 restraints weight = 5153.907| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.7068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3463 Z= 0.231 Angle : 0.834 12.627 4704 Z= 0.435 Chirality : 0.050 0.179 501 Planarity : 0.005 0.049 605 Dihedral : 6.036 28.870 472 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.40 % Favored : 88.12 % Rotamer: Outliers : 2.43 % Allowed : 25.07 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.39), residues: 421 helix: -4.26 (0.53), residues: 26 sheet: -0.39 (0.48), residues: 135 loop : -2.78 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 36 HIS 0.003 0.001 HIS L 61 PHE 0.015 0.001 PHE H 109 TYR 0.018 0.001 TYR L 55 ARG 0.003 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 24 LYS cc_start: 0.3400 (OUTLIER) cc_final: 0.2303 (tmtt) REVERT: L 79 GLN cc_start: 0.1996 (OUTLIER) cc_final: 0.1675 (mm-40) REVERT: L 83 LEU cc_start: 0.6810 (tt) cc_final: 0.6445 (pp) REVERT: L 85 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7295 (tm-30) outliers start: 9 outliers final: 7 residues processed: 72 average time/residue: 0.1588 time to fit residues: 14.0887 Evaluate side-chains 65 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 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 = 0.3932 r_free = 0.3932 target = 0.107006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.097043 restraints weight = 11513.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.098746 restraints weight = 7368.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.099944 restraints weight = 5231.843| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.7510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 3463 Z= 0.323 Angle : 0.896 12.897 4704 Z= 0.470 Chirality : 0.052 0.227 501 Planarity : 0.006 0.054 605 Dihedral : 6.261 28.517 472 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.48 % Allowed : 14.73 % Favored : 84.80 % Rotamer: Outliers : 2.70 % Allowed : 25.34 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.38), residues: 421 helix: -4.31 (0.51), residues: 26 sheet: -0.07 (0.49), residues: 120 loop : -2.99 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 36 HIS 0.002 0.001 HIS L 61 PHE 0.021 0.002 PHE A 392 TYR 0.027 0.002 TYR L 55 ARG 0.003 0.001 ARG A 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 62 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7387 (tm-30) REVERT: L 24 LYS cc_start: 0.3098 (OUTLIER) cc_final: 0.1876 (tmtt) REVERT: L 55 TYR cc_start: 0.3647 (OUTLIER) cc_final: 0.2030 (m-10) REVERT: L 85 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7286 (tm-30) outliers start: 10 outliers final: 8 residues processed: 63 average time/residue: 0.1466 time to fit residues: 11.6995 Evaluate side-chains 61 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 55 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 6.9990 chunk 11 optimal weight: 0.0670 chunk 14 optimal weight: 0.0170 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 42 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 = 0.3987 r_free = 0.3987 target = 0.110255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.100974 restraints weight = 11797.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.102684 restraints weight = 7277.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.103889 restraints weight = 5068.308| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.7394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3463 Z= 0.216 Angle : 0.827 12.880 4704 Z= 0.427 Chirality : 0.050 0.218 501 Planarity : 0.005 0.041 605 Dihedral : 5.779 23.715 472 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.93 % Favored : 88.60 % Rotamer: Outliers : 3.23 % Allowed : 24.80 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.38), residues: 421 helix: -4.20 (0.54), residues: 26 sheet: -0.33 (0.47), residues: 134 loop : -2.85 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 36 HIS 0.003 0.001 HIS L 61 PHE 0.015 0.001 PHE H 109 TYR 0.012 0.001 TYR L 55 ARG 0.005 0.001 ARG A 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1610.98 seconds wall clock time: 28 minutes 41.72 seconds (1721.72 seconds total)