Starting phenix.real_space_refine on Wed Mar 5 22:57:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dt3_27690/03_2025/8dt3_27690_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dt3_27690/03_2025/8dt3_27690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dt3_27690/03_2025/8dt3_27690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dt3_27690/03_2025/8dt3_27690.map" model { file = "/net/cci-nas-00/data/ceres_data/8dt3_27690/03_2025/8dt3_27690_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dt3_27690/03_2025/8dt3_27690_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 18 5.16 5 C 2416 2.51 5 N 636 2.21 5 O 751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3821 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 2005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2005 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 13, 'TRANS': 239} Chain breaks: 1 Chain: "H" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 927 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "L" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 851 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "T" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.40, per 1000 atoms: 0.89 Number of scatterers: 3821 At special positions: 0 Unit cell: (59.4, 97.2, 104.76, 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 18 16.00 O 751 8.00 N 636 7.00 C 2416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 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 24 " - pdb=" SG CYS L 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG T 1 " - " NAG T 2 " BETA1-6 " NAG T 1 " - " FUC T 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG T 1 " - " ASN C 343 " Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 784.1 milliseconds 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 890 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 9 sheets defined 12.4% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.936A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.794A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.296A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.783A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.925A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.547A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.047A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'C' and resid 538 through 543 removed outlier: 5.710A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.218A pdb=" N GLU H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TRP H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N MET H 34 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.218A pdb=" N GLU H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N CYS H 96 " --> pdb=" O TRP H 111 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TRP H 111 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ARG H 98 " --> pdb=" O ASP H 109 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AA9, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.924A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) 127 hydrogen bonds defined for protein. 291 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: 1.34 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1220 1.35 - 1.47: 1054 1.47 - 1.60: 1612 1.60 - 1.72: 0 1.72 - 1.85: 22 Bond restraints: 3908 Sorted by residual: bond pdb=" C1 FUC T 3 " pdb=" C2 FUC T 3 " ideal model delta sigma weight residual 1.528 1.576 -0.048 2.00e-02 2.50e+03 5.81e+00 bond pdb=" N ASP H 57 " pdb=" CA ASP H 57 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.28e-02 6.10e+03 5.58e+00 bond pdb=" C2 FUC T 3 " pdb=" C3 FUC T 3 " ideal model delta sigma weight residual 1.526 1.554 -0.028 2.00e-02 2.50e+03 2.02e+00 bond pdb=" C ALA C 520 " pdb=" N PRO C 521 " ideal model delta sigma weight residual 1.330 1.346 -0.016 1.19e-02 7.06e+03 1.75e+00 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.70e+00 ... (remaining 3903 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 5120 1.59 - 3.18: 141 3.18 - 4.78: 31 4.78 - 6.37: 7 6.37 - 7.96: 2 Bond angle restraints: 5301 Sorted by residual: angle pdb=" C TYR L 51 " pdb=" N THR L 52 " pdb=" CA THR L 52 " ideal model delta sigma weight residual 121.54 129.01 -7.47 1.91e+00 2.74e-01 1.53e+01 angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 122.36 -7.96 2.30e+00 1.89e-01 1.20e+01 angle pdb=" C GLY C 431 " pdb=" N CYS C 432 " pdb=" CA CYS C 432 " ideal model delta sigma weight residual 122.10 116.63 5.47 1.66e+00 3.63e-01 1.09e+01 angle pdb=" CA GLY C 431 " pdb=" C GLY C 431 " pdb=" O GLY C 431 " ideal model delta sigma weight residual 122.65 118.60 4.05 1.28e+00 6.10e-01 1.00e+01 angle pdb=" N GLY C 431 " pdb=" CA GLY C 431 " pdb=" C GLY C 431 " ideal model delta sigma weight residual 112.58 106.99 5.59 1.80e+00 3.09e-01 9.63e+00 ... (remaining 5296 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.93: 2212 23.93 - 47.87: 93 47.87 - 71.80: 21 71.80 - 95.73: 13 95.73 - 119.67: 9 Dihedral angle restraints: 2348 sinusoidal: 950 harmonic: 1398 Sorted by residual: dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 37.63 55.37 1 1.00e+01 1.00e-02 4.14e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 46.59 46.41 1 1.00e+01 1.00e-02 2.98e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 54.16 38.84 1 1.00e+01 1.00e-02 2.12e+01 ... (remaining 2345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 358 0.032 - 0.064: 142 0.064 - 0.095: 47 0.095 - 0.127: 34 0.127 - 0.159: 6 Chirality restraints: 587 Sorted by residual: chirality pdb=" CA ILE C 434 " pdb=" N ILE C 434 " pdb=" C ILE C 434 " pdb=" CB ILE C 434 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" C5 NAG T 1 " pdb=" C4 NAG T 1 " pdb=" C6 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.41 -2.56 0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA ILE L 76 " pdb=" N ILE L 76 " pdb=" C ILE L 76 " pdb=" CB ILE L 76 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 584 not shown) Planarity restraints: 680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG H 40 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.73e+00 pdb=" N PRO H 41 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 369 " -0.014 2.00e-02 2.50e+03 1.01e-02 2.06e+00 pdb=" CG TYR C 369 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR C 369 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 369 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 369 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 369 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 369 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 369 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 54 " -0.098 9.50e-02 1.11e+02 4.40e-02 1.51e+00 pdb=" NE ARG L 54 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG L 54 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG L 54 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG L 54 " -0.000 2.00e-02 2.50e+03 ... (remaining 677 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 104 2.68 - 3.24: 3777 3.24 - 3.79: 5799 3.79 - 4.35: 7951 4.35 - 4.90: 13135 Nonbonded interactions: 30766 Sorted by model distance: nonbonded pdb=" O SER L 31 " pdb=" OH TYR L 72 " model vdw 2.125 3.040 nonbonded pdb=" OG SER C 469 " pdb=" OE1 GLU C 471 " model vdw 2.225 3.040 nonbonded pdb=" OG SER C 530 " pdb=" OE1 GLN C 580 " model vdw 2.251 3.040 nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.255 3.040 nonbonded pdb=" NE2 HIS L 56 " pdb=" O3 FUC T 3 " model vdw 2.262 3.120 ... (remaining 30761 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.160 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 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 : 0.004 0.048 3908 Z= 0.239 Angle : 0.666 7.961 5301 Z= 0.357 Chirality : 0.045 0.159 587 Planarity : 0.004 0.065 679 Dihedral : 17.521 119.666 1440 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.40), residues: 477 helix: -3.69 (0.56), residues: 34 sheet: 0.93 (0.41), residues: 177 loop : -0.95 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 33 HIS 0.002 0.001 HIS L 56 PHE 0.013 0.001 PHE C 392 TYR 0.025 0.002 TYR C 369 ARG 0.010 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.442 Fit side-chains REVERT: C 365 TYR cc_start: 0.5792 (p90) cc_final: 0.5403 (p90) REVERT: H 80 TYR cc_start: 0.8183 (m-80) cc_final: 0.7937 (m-80) REVERT: L 105 LEU cc_start: 0.9313 (mp) cc_final: 0.8676 (mp) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1612 time to fit residues: 13.6726 Evaluate side-chains 58 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 22 optimal weight: 0.0270 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.076327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.061584 restraints weight = 12832.750| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.83 r_work: 0.3100 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3908 Z= 0.203 Angle : 0.644 8.673 5301 Z= 0.325 Chirality : 0.045 0.155 587 Planarity : 0.004 0.042 679 Dihedral : 13.002 120.736 585 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.24 % Allowed : 8.13 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.40), residues: 477 helix: -3.55 (0.71), residues: 27 sheet: 1.14 (0.43), residues: 163 loop : -0.87 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 33 HIS 0.003 0.001 HIS L 56 PHE 0.012 0.001 PHE C 392 TYR 0.022 0.001 TYR C 369 ARG 0.005 0.001 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: C 358 ILE cc_start: 0.8658 (mm) cc_final: 0.8439 (mt) REVERT: C 365 TYR cc_start: 0.6114 (p90) cc_final: 0.5896 (p90) REVERT: C 563 GLN cc_start: 0.8347 (mt0) cc_final: 0.7449 (mm110) REVERT: H 80 TYR cc_start: 0.8500 (m-80) cc_final: 0.8204 (m-80) REVERT: L 80 GLU cc_start: 0.8854 (tt0) cc_final: 0.8602 (tt0) REVERT: L 81 GLN cc_start: 0.8599 (tp-100) cc_final: 0.8327 (tp-100) REVERT: L 82 GLU cc_start: 0.8667 (pm20) cc_final: 0.8166 (pm20) REVERT: L 87 TYR cc_start: 0.8816 (m-80) cc_final: 0.8595 (m-80) outliers start: 1 outliers final: 1 residues processed: 65 average time/residue: 0.1512 time to fit residues: 12.6835 Evaluate side-chains 60 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 34 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 35 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 37 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.075148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.060277 restraints weight = 12926.454| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.84 r_work: 0.3080 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3908 Z= 0.250 Angle : 0.611 8.918 5301 Z= 0.312 Chirality : 0.045 0.186 587 Planarity : 0.004 0.036 679 Dihedral : 10.779 104.828 585 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 1.44 % Allowed : 10.53 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.40), residues: 477 helix: -3.40 (0.69), residues: 33 sheet: 1.26 (0.43), residues: 161 loop : -0.84 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 33 HIS 0.003 0.001 HIS L 56 PHE 0.010 0.001 PHE C 392 TYR 0.018 0.001 TYR C 369 ARG 0.006 0.001 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: C 358 ILE cc_start: 0.8710 (mm) cc_final: 0.8485 (mt) REVERT: C 365 TYR cc_start: 0.6147 (p90) cc_final: 0.5791 (p90) REVERT: C 493 GLN cc_start: 0.8206 (mp10) cc_final: 0.7969 (mp10) REVERT: C 563 GLN cc_start: 0.8375 (mt0) cc_final: 0.7580 (mm110) REVERT: H 80 TYR cc_start: 0.8527 (m-80) cc_final: 0.8268 (m-80) REVERT: L 80 GLU cc_start: 0.8777 (tt0) cc_final: 0.8248 (tt0) REVERT: L 82 GLU cc_start: 0.8623 (pm20) cc_final: 0.7952 (pm20) outliers start: 6 outliers final: 6 residues processed: 59 average time/residue: 0.1607 time to fit residues: 12.2185 Evaluate side-chains 61 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 1 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.075030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.059869 restraints weight = 12887.822| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.86 r_work: 0.3072 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3908 Z= 0.251 Angle : 0.607 9.025 5301 Z= 0.311 Chirality : 0.045 0.165 587 Planarity : 0.004 0.034 679 Dihedral : 10.383 98.659 585 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.91 % Allowed : 10.77 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.39), residues: 477 helix: -3.48 (0.65), residues: 34 sheet: 1.23 (0.43), residues: 156 loop : -0.84 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 33 HIS 0.003 0.001 HIS L 56 PHE 0.009 0.001 PHE C 392 TYR 0.016 0.001 TYR C 369 ARG 0.007 0.001 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: C 358 ILE cc_start: 0.8715 (mm) cc_final: 0.8488 (mt) REVERT: C 365 TYR cc_start: 0.6099 (p90) cc_final: 0.5770 (p90) REVERT: C 434 ILE cc_start: 0.9495 (mt) cc_final: 0.9280 (mt) REVERT: C 493 GLN cc_start: 0.8167 (mp10) cc_final: 0.7911 (mp10) REVERT: C 563 GLN cc_start: 0.8392 (mt0) cc_final: 0.7650 (mm110) REVERT: H 80 TYR cc_start: 0.8549 (m-80) cc_final: 0.8307 (m-80) REVERT: L 80 GLU cc_start: 0.8816 (tt0) cc_final: 0.8322 (tt0) REVERT: L 82 GLU cc_start: 0.8564 (pm20) cc_final: 0.7854 (pm20) outliers start: 8 outliers final: 7 residues processed: 61 average time/residue: 0.1443 time to fit residues: 11.3148 Evaluate side-chains 63 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 0.0970 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.074048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.059014 restraints weight = 13177.485| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.86 r_work: 0.3057 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3908 Z= 0.268 Angle : 0.617 9.223 5301 Z= 0.315 Chirality : 0.046 0.180 587 Planarity : 0.004 0.032 679 Dihedral : 9.926 92.899 585 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.63 % Allowed : 12.20 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.39), residues: 477 helix: -3.46 (0.64), residues: 34 sheet: 1.18 (0.43), residues: 157 loop : -0.88 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 33 HIS 0.003 0.001 HIS L 56 PHE 0.013 0.001 PHE C 559 TYR 0.016 0.001 TYR C 369 ARG 0.007 0.000 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: C 358 ILE cc_start: 0.8715 (mm) cc_final: 0.8477 (mt) REVERT: C 434 ILE cc_start: 0.9527 (mt) cc_final: 0.9314 (mt) REVERT: C 493 GLN cc_start: 0.8224 (mp10) cc_final: 0.8005 (mp10) REVERT: C 559 PHE cc_start: 0.2890 (OUTLIER) cc_final: 0.1861 (m-80) REVERT: C 563 GLN cc_start: 0.8552 (mt0) cc_final: 0.7567 (mm110) REVERT: H 80 TYR cc_start: 0.8592 (m-80) cc_final: 0.8369 (m-80) REVERT: L 80 GLU cc_start: 0.8825 (tt0) cc_final: 0.8348 (tt0) REVERT: L 81 GLN cc_start: 0.8549 (tp-100) cc_final: 0.8304 (tp-100) outliers start: 11 outliers final: 9 residues processed: 62 average time/residue: 0.1518 time to fit residues: 12.2038 Evaluate side-chains 66 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.074461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.059587 restraints weight = 12758.514| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.79 r_work: 0.3072 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3908 Z= 0.242 Angle : 0.626 9.033 5301 Z= 0.316 Chirality : 0.046 0.176 587 Planarity : 0.003 0.030 679 Dihedral : 9.349 86.818 585 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.63 % Allowed : 14.35 % Favored : 83.01 % 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: -0.50 (0.39), residues: 477 helix: -3.34 (0.66), residues: 33 sheet: 1.20 (0.44), residues: 157 loop : -0.87 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 33 HIS 0.002 0.001 HIS L 56 PHE 0.007 0.001 PHE C 392 TYR 0.016 0.001 TYR C 365 ARG 0.007 0.000 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 358 ILE cc_start: 0.8669 (mm) cc_final: 0.8431 (mt) REVERT: C 434 ILE cc_start: 0.9525 (mt) cc_final: 0.9312 (mt) REVERT: C 493 GLN cc_start: 0.8186 (mp10) cc_final: 0.7932 (mp10) REVERT: C 563 GLN cc_start: 0.8478 (mt0) cc_final: 0.7938 (mm110) REVERT: H 80 TYR cc_start: 0.8584 (m-80) cc_final: 0.8359 (m-80) REVERT: L 80 GLU cc_start: 0.8802 (tt0) cc_final: 0.8354 (tt0) outliers start: 11 outliers final: 9 residues processed: 65 average time/residue: 0.1537 time to fit residues: 12.7175 Evaluate side-chains 66 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 23 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 44 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.074970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.060101 restraints weight = 12754.058| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 3.80 r_work: 0.3112 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3908 Z= 0.228 Angle : 0.639 9.593 5301 Z= 0.320 Chirality : 0.046 0.173 587 Planarity : 0.004 0.030 679 Dihedral : 8.433 74.684 585 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.35 % Allowed : 14.59 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.39), residues: 477 helix: -3.20 (0.70), residues: 33 sheet: 1.20 (0.44), residues: 157 loop : -0.86 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 33 HIS 0.002 0.001 HIS L 56 PHE 0.015 0.001 PHE C 559 TYR 0.033 0.001 TYR C 365 ARG 0.007 0.000 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: C 358 ILE cc_start: 0.8666 (mm) cc_final: 0.8432 (mt) REVERT: C 434 ILE cc_start: 0.9520 (mt) cc_final: 0.9306 (mt) REVERT: C 493 GLN cc_start: 0.8234 (mp10) cc_final: 0.7997 (mp10) REVERT: C 559 PHE cc_start: 0.3064 (OUTLIER) cc_final: 0.1486 (m-80) REVERT: C 563 GLN cc_start: 0.8398 (mt0) cc_final: 0.7499 (mm110) REVERT: H 80 TYR cc_start: 0.8552 (m-80) cc_final: 0.8331 (m-80) REVERT: L 80 GLU cc_start: 0.8839 (tt0) cc_final: 0.8337 (tt0) outliers start: 14 outliers final: 11 residues processed: 66 average time/residue: 0.1562 time to fit residues: 13.1178 Evaluate side-chains 67 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.074664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.059837 restraints weight = 12886.519| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.82 r_work: 0.3064 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3908 Z= 0.258 Angle : 0.712 19.407 5301 Z= 0.339 Chirality : 0.046 0.179 587 Planarity : 0.004 0.039 679 Dihedral : 8.017 67.776 585 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.11 % Allowed : 15.79 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.40), residues: 477 helix: -3.03 (0.78), residues: 33 sheet: 1.19 (0.44), residues: 157 loop : -0.84 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 33 HIS 0.002 0.001 HIS L 56 PHE 0.011 0.001 PHE C 559 TYR 0.033 0.002 TYR C 365 ARG 0.009 0.001 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.436 Fit side-chains REVERT: C 358 ILE cc_start: 0.8672 (mm) cc_final: 0.8441 (mt) REVERT: C 434 ILE cc_start: 0.9535 (mt) cc_final: 0.9316 (mt) REVERT: C 493 GLN cc_start: 0.8261 (mp10) cc_final: 0.8043 (mp10) REVERT: C 559 PHE cc_start: 0.3090 (OUTLIER) cc_final: 0.1346 (m-80) REVERT: H 80 TYR cc_start: 0.8595 (m-80) cc_final: 0.8377 (m-80) outliers start: 13 outliers final: 12 residues processed: 62 average time/residue: 0.1374 time to fit residues: 11.3523 Evaluate side-chains 68 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.074601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.059904 restraints weight = 12838.255| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.78 r_work: 0.3069 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3908 Z= 0.261 Angle : 0.692 14.076 5301 Z= 0.337 Chirality : 0.046 0.181 587 Planarity : 0.004 0.043 679 Dihedral : 7.607 60.036 585 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.11 % Allowed : 15.79 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.40), residues: 477 helix: -3.09 (0.76), residues: 33 sheet: 1.17 (0.44), residues: 157 loop : -0.85 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 33 HIS 0.002 0.001 HIS L 56 PHE 0.016 0.001 PHE C 562 TYR 0.029 0.002 TYR C 365 ARG 0.008 0.001 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.467 Fit side-chains REVERT: C 358 ILE cc_start: 0.8671 (mm) cc_final: 0.8441 (mt) REVERT: C 434 ILE cc_start: 0.9534 (mt) cc_final: 0.9314 (mt) REVERT: C 493 GLN cc_start: 0.8277 (mp10) cc_final: 0.8027 (mp10) REVERT: C 516 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7629 (tm-30) REVERT: C 559 PHE cc_start: 0.3306 (OUTLIER) cc_final: 0.1680 (m-80) REVERT: H 80 TYR cc_start: 0.8599 (m-80) cc_final: 0.8381 (m-80) outliers start: 13 outliers final: 12 residues processed: 60 average time/residue: 0.1409 time to fit residues: 11.3186 Evaluate side-chains 67 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 17 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 0.0270 chunk 1 optimal weight: 0.6980 chunk 14 optimal weight: 0.0870 chunk 42 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 overall best weight: 0.3816 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.076090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.061309 restraints weight = 12699.490| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.80 r_work: 0.3101 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3908 Z= 0.187 Angle : 0.688 12.904 5301 Z= 0.339 Chirality : 0.045 0.177 587 Planarity : 0.004 0.042 679 Dihedral : 6.808 50.916 585 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.87 % Allowed : 16.03 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.40), residues: 477 helix: -3.13 (0.75), residues: 33 sheet: 1.22 (0.44), residues: 157 loop : -0.82 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 33 HIS 0.001 0.000 HIS L 93 PHE 0.011 0.001 PHE C 559 TYR 0.026 0.001 TYR C 369 ARG 0.007 0.001 ARG L 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.494 Fit side-chains REVERT: C 358 ILE cc_start: 0.8616 (mm) cc_final: 0.8389 (mt) REVERT: C 434 ILE cc_start: 0.9523 (mt) cc_final: 0.9312 (mt) REVERT: C 493 GLN cc_start: 0.8216 (mp10) cc_final: 0.7971 (mp10) REVERT: C 516 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7496 (tm-30) REVERT: C 559 PHE cc_start: 0.3416 (OUTLIER) cc_final: 0.1725 (m-80) REVERT: H 80 TYR cc_start: 0.8503 (m-80) cc_final: 0.8278 (m-80) outliers start: 12 outliers final: 10 residues processed: 61 average time/residue: 0.1402 time to fit residues: 11.0868 Evaluate side-chains 66 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 24 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.075656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.060490 restraints weight = 12603.125| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.84 r_work: 0.3081 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3908 Z= 0.219 Angle : 0.681 11.446 5301 Z= 0.337 Chirality : 0.046 0.192 587 Planarity : 0.004 0.041 679 Dihedral : 6.796 52.051 585 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.87 % Allowed : 16.51 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.40), residues: 477 helix: -3.18 (0.74), residues: 33 sheet: 1.20 (0.44), residues: 157 loop : -0.78 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 33 HIS 0.002 0.001 HIS L 56 PHE 0.011 0.001 PHE C 559 TYR 0.024 0.001 TYR C 365 ARG 0.010 0.001 ARG L 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2236.72 seconds wall clock time: 39 minutes 14.49 seconds (2354.49 seconds total)