Starting phenix.real_space_refine on Tue Feb 11 00:42:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f63_31471/02_2025/7f63_31471.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f63_31471/02_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_31471/02_2025/7f63_31471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f63_31471/02_2025/7f63_31471.map" model { file = "/net/cci-nas-00/data/ceres_data/7f63_31471/02_2025/7f63_31471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f63_31471/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 3.30, per 1000 atoms: 0.98 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: 0.69 Conformation dependent library (CDL) restraints added in 451.0 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: 0.38 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: 0.82 Time building geometry restraints manager: 0.85 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: 2.310 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.440 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.030 ------------------------------------------------------------------------------- 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 : 0.395 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: 0.2295 time to fit residues: 30.8430 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 : 0.367 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.110273 restraints weight = 7572.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.111519 restraints weight = 5313.721| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 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 : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLN cc_start: 0.8070 (mp10) cc_final: 0.7719 (mp10) outliers start: 7 outliers final: 2 residues processed: 86 average time/residue: 0.1803 time to fit residues: 18.4481 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 : 0.427 ------------------------------------------------------------------------------- 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: 0.8980 chunk 33 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 L 61 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.112151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.101240 restraints weight = 11259.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.103036 restraints weight = 7302.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.104300 restraints weight = 5220.806| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3463 Z= 0.196 Angle : 0.694 11.723 4704 Z= 0.364 Chirality : 0.047 0.213 501 Planarity : 0.004 0.035 605 Dihedral : 5.173 17.462 472 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.98 % Favored : 89.55 % Rotamer: Outliers : 3.23 % Allowed : 17.25 % Favored : 79.51 % 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: -2.32 (0.40), residues: 421 helix: -3.20 (0.91), residues: 20 sheet: 0.22 (0.48), residues: 136 loop : -2.54 (0.34), residues: 265 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 0.018 0.002 PHE H 29 TYR 0.014 0.001 TYR H 80 ARG 0.005 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: 12 poor density : 74 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 33 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.8914 (t) REVERT: H 62 GLN cc_start: 0.7432 (tm-30) cc_final: 0.7123 (tm-30) REVERT: L 83 LEU cc_start: 0.6894 (tt) cc_final: 0.6577 (pp) REVERT: L 85 GLU cc_start: 0.7359 (tp30) cc_final: 0.7089 (tm-30) REVERT: L 91 TYR cc_start: 0.8521 (p90) cc_final: 0.8016 (p90) outliers start: 12 outliers final: 8 residues processed: 83 average time/residue: 0.1876 time to fit residues: 18.2929 Evaluate side-chains 66 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 2.9990 chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.111533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.100639 restraints weight = 11385.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.102521 restraints weight = 7374.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.103797 restraints weight = 5220.962| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3463 Z= 0.216 Angle : 0.721 11.577 4704 Z= 0.375 Chirality : 0.047 0.215 501 Planarity : 0.004 0.038 605 Dihedral : 5.405 20.046 472 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.64 % Favored : 87.89 % Rotamer: Outliers : 2.43 % Allowed : 20.75 % Favored : 76.82 % 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: -2.30 (0.40), residues: 421 helix: -3.45 (0.83), residues: 20 sheet: 0.29 (0.50), residues: 130 loop : -2.49 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.001 0.000 HIS L 61 PHE 0.016 0.001 PHE H 29 TYR 0.014 0.001 TYR H 60 ARG 0.003 0.001 ARG A 408 *********************** 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 73 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 33 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.8926 (t) REVERT: H 62 GLN cc_start: 0.7518 (tm-30) cc_final: 0.7300 (tm-30) REVERT: L 83 LEU cc_start: 0.6858 (tt) cc_final: 0.6456 (pp) REVERT: L 85 GLU cc_start: 0.7618 (tp30) cc_final: 0.7038 (tm-30) REVERT: L 91 TYR cc_start: 0.8558 (p90) cc_final: 0.8139 (p90) outliers start: 9 outliers final: 6 residues processed: 71 average time/residue: 0.1675 time to fit residues: 14.4492 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 : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 33 THR Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 107 LEU 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: 3.9990 chunk 22 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 21 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** 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 = 0.3939 r_free = 0.3939 target = 0.107547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.096765 restraints weight = 11567.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.098598 restraints weight = 7368.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.099851 restraints weight = 5208.418| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.6417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3463 Z= 0.264 Angle : 0.748 11.198 4704 Z= 0.398 Chirality : 0.049 0.200 501 Planarity : 0.006 0.076 605 Dihedral : 5.857 21.401 472 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.40 % Favored : 88.12 % Rotamer: Outliers : 5.66 % Allowed : 19.14 % Favored : 75.20 % 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: -2.61 (0.40), residues: 421 helix: -3.47 (0.63), residues: 26 sheet: 0.11 (0.50), residues: 132 loop : -2.72 (0.34), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 36 HIS 0.001 0.001 HIS L 61 PHE 0.017 0.002 PHE H 63 TYR 0.022 0.002 TYR L 55 ARG 0.003 0.001 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 82 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLN cc_start: 0.8034 (mp10) cc_final: 0.7606 (mp10) REVERT: H 62 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7582 (tm-30) REVERT: L 55 TYR cc_start: 0.3491 (OUTLIER) cc_final: 0.2032 (m-10) REVERT: L 83 LEU cc_start: 0.7153 (tt) cc_final: 0.6724 (pp) outliers start: 21 outliers final: 8 residues processed: 78 average time/residue: 0.1510 time to fit residues: 14.6041 Evaluate side-chains 66 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 364 ASP 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 A residue 525 CYS 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: 2.9990 chunk 12 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 0.0670 chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 0.0980 chunk 1 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3992 r_free = 0.3992 target = 0.110249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.099858 restraints weight = 11729.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.101720 restraints weight = 7248.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.102964 restraints weight = 4999.324| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.6444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3463 Z= 0.190 Angle : 0.713 11.955 4704 Z= 0.372 Chirality : 0.048 0.216 501 Planarity : 0.005 0.050 605 Dihedral : 5.603 24.641 472 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.45 % Favored : 89.07 % Rotamer: Outliers : 1.89 % Allowed : 23.45 % 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: -2.65 (0.39), residues: 421 helix: -3.81 (0.59), residues: 26 sheet: 0.03 (0.49), residues: 131 loop : -2.67 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.003 0.001 HIS L 61 PHE 0.013 0.001 PHE H 29 TYR 0.036 0.002 TYR H 103 ARG 0.003 0.000 ARG L 54 *********************** 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 67 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLN cc_start: 0.8194 (mp10) cc_final: 0.7571 (mp10) REVERT: H 62 GLN cc_start: 0.7721 (tm-30) cc_final: 0.7453 (tm-30) REVERT: L 28 ASN cc_start: 0.7591 (p0) cc_final: 0.7342 (p0) REVERT: L 83 LEU cc_start: 0.7124 (tt) cc_final: 0.6670 (pp) REVERT: L 85 GLU cc_start: 0.7626 (tp30) cc_final: 0.6784 (tm-30) outliers start: 7 outliers final: 2 residues processed: 67 average time/residue: 0.1453 time to fit residues: 12.1610 Evaluate side-chains 55 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 55 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3953 r_free = 0.3953 target = 0.108539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.098160 restraints weight = 11516.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.099900 restraints weight = 7314.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.101113 restraints weight = 5155.331| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.6889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3463 Z= 0.232 Angle : 0.756 12.007 4704 Z= 0.396 Chirality : 0.049 0.208 501 Planarity : 0.005 0.055 605 Dihedral : 5.673 27.372 472 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.88 % Favored : 87.65 % Rotamer: Outliers : 2.16 % Allowed : 24.26 % Favored : 73.58 % 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: -2.85 (0.39), residues: 421 helix: -4.06 (0.57), residues: 26 sheet: -0.08 (0.48), residues: 132 loop : -2.82 (0.34), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.002 0.001 HIS L 61 PHE 0.016 0.002 PHE H 109 TYR 0.037 0.002 TYR H 103 ARG 0.003 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 68 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLN cc_start: 0.7922 (mp10) cc_final: 0.7380 (mp10) REVERT: H 62 GLN cc_start: 0.7896 (tm-30) cc_final: 0.7520 (tm-30) REVERT: H 108 ASP cc_start: 0.7965 (p0) cc_final: 0.7758 (p0) REVERT: L 24 LYS cc_start: 0.3329 (OUTLIER) cc_final: 0.2205 (tmtt) REVERT: L 55 TYR cc_start: 0.3748 (OUTLIER) cc_final: 0.1704 (m-10) REVERT: L 83 LEU cc_start: 0.6888 (tt) cc_final: 0.6547 (pp) REVERT: L 85 GLU cc_start: 0.7753 (tp30) cc_final: 0.6827 (tm-30) outliers start: 8 outliers final: 5 residues processed: 68 average time/residue: 0.1576 time to fit residues: 13.3921 Evaluate side-chains 63 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3986 r_free = 0.3986 target = 0.110149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.100314 restraints weight = 11561.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.102045 restraints weight = 7318.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.103226 restraints weight = 5108.851| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.6954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3463 Z= 0.207 Angle : 0.788 12.361 4704 Z= 0.412 Chirality : 0.048 0.165 501 Planarity : 0.005 0.048 605 Dihedral : 5.897 26.958 472 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.16 % Favored : 88.36 % Rotamer: Outliers : 2.70 % Allowed : 24.80 % 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: -2.91 (0.39), residues: 421 helix: -4.24 (0.53), residues: 26 sheet: -0.09 (0.49), residues: 131 loop : -2.86 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 36 HIS 0.002 0.001 HIS L 61 PHE 0.018 0.001 PHE H 109 TYR 0.018 0.002 TYR L 91 ARG 0.004 0.001 ARG A 408 *********************** 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 71 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLN cc_start: 0.7975 (mp10) cc_final: 0.7444 (mp10) REVERT: H 62 GLN cc_start: 0.7875 (tm-30) cc_final: 0.7485 (tm-30) REVERT: L 24 LYS cc_start: 0.3305 (OUTLIER) cc_final: 0.2214 (tmtt) REVERT: L 28 ASN cc_start: 0.7679 (p0) cc_final: 0.7465 (p0) REVERT: L 79 GLN cc_start: 0.1827 (OUTLIER) cc_final: 0.1537 (mm-40) REVERT: L 83 LEU cc_start: 0.6808 (tt) cc_final: 0.6488 (pp) outliers start: 10 outliers final: 7 residues processed: 71 average time/residue: 0.1467 time to fit residues: 13.0364 Evaluate side-chains 64 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 73 LEU 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: 0.0670 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 0.0770 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3997 r_free = 0.3997 target = 0.110789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.100906 restraints weight = 11333.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.102634 restraints weight = 7169.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.103826 restraints weight = 5051.071| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.7076 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= 0.208 Angle : 0.807 12.534 4704 Z= 0.419 Chirality : 0.048 0.216 501 Planarity : 0.005 0.045 605 Dihedral : 5.893 27.457 472 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.48 % Allowed : 12.83 % Favored : 86.70 % Rotamer: Outliers : 2.96 % Allowed : 24.53 % 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: -2.91 (0.39), residues: 421 helix: -4.27 (0.54), residues: 26 sheet: -0.07 (0.49), residues: 131 loop : -2.87 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.002 0.001 HIS L 61 PHE 0.019 0.001 PHE H 109 TYR 0.020 0.002 TYR H 103 ARG 0.003 0.000 ARG A 408 *********************** 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 69 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLN cc_start: 0.8163 (mp10) cc_final: 0.7602 (mp10) REVERT: H 62 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7445 (tm-30) REVERT: H 103 TYR cc_start: 0.5462 (t80) cc_final: 0.4875 (t80) REVERT: L 24 LYS cc_start: 0.3184 (OUTLIER) cc_final: 0.2181 (tmtt) REVERT: L 28 ASN cc_start: 0.7606 (p0) cc_final: 0.7386 (p0) REVERT: L 79 GLN cc_start: 0.1817 (OUTLIER) cc_final: 0.1586 (mm-40) REVERT: L 83 LEU cc_start: 0.6870 (tt) cc_final: 0.6527 (pp) REVERT: L 85 GLU cc_start: 0.7688 (tp30) cc_final: 0.6685 (tm-30) outliers start: 11 outliers final: 8 residues processed: 67 average time/residue: 0.1391 time to fit residues: 11.7383 Evaluate side-chains 67 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 3 GLN 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 73 LEU 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: 0.8980 chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3960 r_free = 0.3960 target = 0.108320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.098376 restraints weight = 11504.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.100119 restraints weight = 7267.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.101322 restraints weight = 5105.357| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.7397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3463 Z= 0.265 Angle : 0.865 12.803 4704 Z= 0.453 Chirality : 0.050 0.221 501 Planarity : 0.005 0.052 605 Dihedral : 6.236 28.133 472 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.48 % Allowed : 13.54 % Favored : 85.99 % Rotamer: Outliers : 2.96 % Allowed : 25.07 % 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: -3.05 (0.39), residues: 421 helix: -4.43 (0.46), residues: 26 sheet: -0.11 (0.49), residues: 131 loop : -2.99 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.002 0.001 HIS L 61 PHE 0.025 0.002 PHE H 63 TYR 0.021 0.002 TYR L 55 ARG 0.003 0.001 ARG A 408 ********************** 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 70 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 CYS cc_start: 0.2636 (p) cc_final: 0.2388 (p) REVERT: A 498 GLN cc_start: 0.7957 (mp10) cc_final: 0.7394 (mp10) REVERT: H 62 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7543 (tm-30) REVERT: L 24 LYS cc_start: 0.3221 (OUTLIER) cc_final: 0.2148 (tmtt) REVERT: L 28 ASN cc_start: 0.7583 (p0) cc_final: 0.7369 (p0) REVERT: L 55 TYR cc_start: 0.3900 (OUTLIER) cc_final: 0.1839 (m-10) REVERT: L 79 GLN cc_start: 0.2116 (OUTLIER) cc_final: 0.0076 (mt0) outliers start: 11 outliers final: 5 residues processed: 70 average time/residue: 0.1259 time to fit residues: 11.4155 Evaluate side-chains 66 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 13 optimal weight: 0.0170 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.0870 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4007 r_free = 0.4007 target = 0.111094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.101437 restraints weight = 11831.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.103279 restraints weight = 7168.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.104542 restraints weight = 4885.312| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.7384 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= 0.218 Angle : 0.827 12.668 4704 Z= 0.429 Chirality : 0.049 0.220 501 Planarity : 0.005 0.042 605 Dihedral : 5.970 27.535 472 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.48 % Allowed : 12.59 % Favored : 86.94 % Rotamer: Outliers : 1.89 % Allowed : 25.61 % 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: -3.08 (0.38), residues: 421 helix: -4.44 (0.46), residues: 26 sheet: -0.26 (0.48), residues: 132 loop : -2.95 (0.33), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 35 HIS 0.002 0.001 HIS L 61 PHE 0.020 0.001 PHE H 109 TYR 0.012 0.001 TYR L 55 ARG 0.003 0.000 ARG H 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1622.27 seconds wall clock time: 29 minutes 51.61 seconds (1791.61 seconds total)