Starting phenix.real_space_refine on Tue Feb 13 06:52:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dt3_27690/02_2024/8dt3_27690_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dt3_27690/02_2024/8dt3_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dt3_27690/02_2024/8dt3_27690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dt3_27690/02_2024/8dt3_27690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dt3_27690/02_2024/8dt3_27690_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dt3_27690/02_2024/8dt3_27690_neut.pdb" } 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 Residue "C GLU 340": "OE1" <-> "OE2" Residue "C GLU 465": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 2.64, per 1000 atoms: 0.69 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 - 3.50 Amino acid : False - 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: 1.58 Conformation dependent library (CDL) restraints added in 836.0 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: 0.50 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: 1.17 Time building geometry restraints manager: 1.70 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: 99.34 - 106.28: 88 106.28 - 113.21: 2063 113.21 - 120.14: 1320 120.14 - 127.07: 1790 127.07 - 134.01: 40 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 2.440 nonbonded pdb=" OG SER C 469 " pdb=" OE1 GLU C 471 " model vdw 2.225 2.440 nonbonded pdb=" OG SER C 530 " pdb=" OE1 GLN C 580 " model vdw 2.251 2.440 nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.255 2.440 nonbonded pdb=" NE2 HIS L 56 " pdb=" O3 FUC T 3 " model vdw 2.262 2.520 ... (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 ========== 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: 1.830 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: 5.540 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.320 Find NCS groups from input model: 0.110 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.470 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.466 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: 0.1557 time to fit residues: 13.2108 Evaluate side-chains 58 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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: 0.9980 chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.0980 chunk 22 optimal weight: 0.0670 chunk 27 optimal weight: 0.6980 chunk 42 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.0931 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= 0.175 Angle : 0.631 9.096 5301 Z= 0.312 Chirality : 0.045 0.157 587 Planarity : 0.004 0.042 679 Dihedral : 14.296 120.792 585 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.48 % Allowed : 8.85 % Favored : 90.67 % 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: -3.45 (0.65), residues: 33 sheet: 1.21 (0.43), residues: 161 loop : -0.80 (0.39), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 33 HIS 0.002 0.001 HIS L 56 PHE 0.009 0.001 PHE C 392 TYR 0.021 0.001 TYR C 369 ARG 0.006 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 fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: C 471 GLU cc_start: 0.8116 (mp0) cc_final: 0.7836 (mp0) REVERT: C 563 GLN cc_start: 0.8332 (mt0) cc_final: 0.7618 (mm110) REVERT: H 80 TYR cc_start: 0.8141 (m-80) cc_final: 0.7864 (m-80) REVERT: L 80 GLU cc_start: 0.8653 (tt0) cc_final: 0.8036 (tt0) REVERT: L 82 GLU cc_start: 0.8420 (pm20) cc_final: 0.7729 (pm20) outliers start: 2 outliers final: 2 residues processed: 65 average time/residue: 0.1398 time to fit residues: 11.7543 Evaluate side-chains 62 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 571 ASP 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 13 optimal weight: 0.0870 chunk 35 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 14 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1217 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= 0.184 Angle : 0.570 8.417 5301 Z= 0.291 Chirality : 0.044 0.191 587 Planarity : 0.003 0.035 679 Dihedral : 11.137 109.192 585 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 1.20 % Allowed : 10.29 % Favored : 88.52 % 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: -0.41 (0.40), residues: 477 helix: -3.47 (0.67), residues: 33 sheet: 1.34 (0.44), residues: 155 loop : -0.82 (0.38), residues: 289 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 0.009 0.001 PHE C 565 TYR 0.010 0.001 TYR C 489 ARG 0.005 0.000 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 69 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.440 Fit side-chains REVERT: C 358 ILE cc_start: 0.8587 (mm) cc_final: 0.8370 (mt) REVERT: C 365 TYR cc_start: 0.5835 (p90) cc_final: 0.5493 (p90) REVERT: C 493 GLN cc_start: 0.7891 (mp10) cc_final: 0.7686 (mp10) REVERT: C 563 GLN cc_start: 0.8323 (mt0) cc_final: 0.7644 (mm110) REVERT: H 80 TYR cc_start: 0.8201 (m-80) cc_final: 0.7955 (m-80) REVERT: H 108 MET cc_start: 0.9057 (mtm) cc_final: 0.8809 (mtm) REVERT: L 37 TYR cc_start: 0.8786 (m-80) cc_final: 0.8422 (m-80) REVERT: L 80 GLU cc_start: 0.8566 (tt0) cc_final: 0.7994 (tt0) REVERT: L 82 GLU cc_start: 0.8379 (pm20) cc_final: 0.7581 (pm20) outliers start: 5 outliers final: 5 residues processed: 65 average time/residue: 0.1437 time to fit residues: 12.0104 Evaluate side-chains 63 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 571 ASP 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 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 3908 Z= 0.369 Angle : 0.645 10.029 5301 Z= 0.330 Chirality : 0.046 0.191 587 Planarity : 0.004 0.034 679 Dihedral : 11.013 102.975 585 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 2.39 % Allowed : 11.96 % Favored : 85.65 % 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: -0.57 (0.39), residues: 477 helix: -3.46 (0.67), residues: 34 sheet: 1.21 (0.44), residues: 156 loop : -0.93 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 33 HIS 0.005 0.001 HIS L 56 PHE 0.012 0.002 PHE C 559 TYR 0.013 0.002 TYR C 489 ARG 0.005 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 fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.460 Fit side-chains REVERT: C 358 ILE cc_start: 0.8639 (mm) cc_final: 0.8395 (mt) REVERT: C 563 GLN cc_start: 0.8557 (mt0) cc_final: 0.8124 (mm-40) REVERT: H 80 TYR cc_start: 0.8394 (m-80) cc_final: 0.8186 (m-80) REVERT: L 80 GLU cc_start: 0.8599 (tt0) cc_final: 0.8222 (tt0) REVERT: L 82 GLU cc_start: 0.8392 (pm20) cc_final: 0.7487 (pm20) outliers start: 10 outliers final: 9 residues processed: 60 average time/residue: 0.1733 time to fit residues: 13.4394 Evaluate side-chains 59 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 571 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3908 Z= 0.302 Angle : 0.625 9.553 5301 Z= 0.319 Chirality : 0.045 0.183 587 Planarity : 0.003 0.034 679 Dihedral : 10.472 96.161 585 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 2.87 % Allowed : 12.20 % Favored : 84.93 % 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: -0.59 (0.39), residues: 477 helix: -3.44 (0.67), residues: 34 sheet: 1.11 (0.44), residues: 156 loop : -0.89 (0.37), 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 0.014 0.002 PHE C 559 TYR 0.028 0.002 TYR C 369 ARG 0.004 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 fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.432 Fit side-chains REVERT: C 358 ILE cc_start: 0.8586 (mm) cc_final: 0.8328 (mt) REVERT: C 365 TYR cc_start: 0.5872 (p90) cc_final: 0.5510 (p90) REVERT: C 563 GLN cc_start: 0.8409 (mt0) cc_final: 0.7591 (mm110) REVERT: L 80 GLU cc_start: 0.8545 (tt0) cc_final: 0.8007 (tt0) REVERT: L 82 GLU cc_start: 0.8379 (pm20) cc_final: 0.7331 (pm20) outliers start: 12 outliers final: 9 residues processed: 62 average time/residue: 0.1670 time to fit residues: 12.9671 Evaluate side-chains 62 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 571 ASP 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 11 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3908 Z= 0.283 Angle : 0.653 11.262 5301 Z= 0.324 Chirality : 0.046 0.184 587 Planarity : 0.004 0.032 679 Dihedral : 10.048 91.908 585 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 3.11 % Allowed : 14.35 % Favored : 82.54 % 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: -0.58 (0.39), residues: 477 helix: -3.42 (0.67), residues: 34 sheet: 1.03 (0.44), residues: 156 loop : -0.83 (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 0.014 0.001 PHE C 559 TYR 0.026 0.002 TYR C 369 ARG 0.008 0.001 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 67 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 0.469 Fit side-chains REVERT: C 358 ILE cc_start: 0.8594 (mm) cc_final: 0.8334 (mt) REVERT: C 365 TYR cc_start: 0.5754 (p90) cc_final: 0.5364 (p90) REVERT: C 563 GLN cc_start: 0.8368 (mt0) cc_final: 0.7641 (mm110) REVERT: L 80 GLU cc_start: 0.8592 (tt0) cc_final: 0.8057 (tt0) REVERT: L 82 GLU cc_start: 0.8342 (pm20) cc_final: 0.7264 (pm20) outliers start: 13 outliers final: 11 residues processed: 61 average time/residue: 0.1516 time to fit residues: 11.9744 Evaluate side-chains 63 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 571 ASP 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 25 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1889 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= 0.241 Angle : 0.632 9.133 5301 Z= 0.315 Chirality : 0.045 0.175 587 Planarity : 0.004 0.031 679 Dihedral : 9.102 81.043 585 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 3.83 % Allowed : 14.59 % Favored : 81.58 % 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: -0.57 (0.40), residues: 477 helix: -3.29 (0.70), residues: 34 sheet: 1.01 (0.44), residues: 156 loop : -0.82 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 33 HIS 0.002 0.001 HIS L 56 PHE 0.012 0.001 PHE C 559 TYR 0.025 0.002 TYR C 369 ARG 0.008 0.001 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 70 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 54 time to evaluate : 0.421 Fit side-chains REVERT: C 358 ILE cc_start: 0.8562 (mm) cc_final: 0.8313 (mt) REVERT: C 365 TYR cc_start: 0.5793 (p90) cc_final: 0.5370 (p90) REVERT: C 559 PHE cc_start: 0.3167 (OUTLIER) cc_final: 0.1720 (m-80) REVERT: C 563 GLN cc_start: 0.8295 (mt0) cc_final: 0.7255 (mm110) REVERT: L 80 GLU cc_start: 0.8565 (tt0) cc_final: 0.8064 (tt0) REVERT: L 82 GLU cc_start: 0.8276 (pm20) cc_final: 0.7175 (pm20) outliers start: 16 outliers final: 12 residues processed: 61 average time/residue: 0.1434 time to fit residues: 11.2283 Evaluate side-chains 65 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 560 LEU Chi-restraints excluded: chain C residue 571 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 0.6980 chunk 35 optimal weight: 0.2980 chunk 41 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 39 optimal weight: 0.0370 chunk 42 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1925 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= 0.185 Angle : 0.629 10.353 5301 Z= 0.309 Chirality : 0.044 0.171 587 Planarity : 0.004 0.028 679 Dihedral : 7.804 62.267 585 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.83 % Allowed : 14.83 % Favored : 81.34 % 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 (0.40), residues: 477 helix: -3.20 (0.80), residues: 27 sheet: 1.11 (0.44), residues: 155 loop : -0.87 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 33 HIS 0.001 0.000 HIS L 56 PHE 0.010 0.001 PHE C 559 TYR 0.024 0.001 TYR C 369 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 74 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 58 time to evaluate : 0.469 Fit side-chains REVERT: C 358 ILE cc_start: 0.8517 (mm) cc_final: 0.8274 (mt) REVERT: C 365 TYR cc_start: 0.5697 (p90) cc_final: 0.5398 (p90) REVERT: C 559 PHE cc_start: 0.3235 (OUTLIER) cc_final: 0.1771 (m-80) REVERT: C 563 GLN cc_start: 0.8264 (mt0) cc_final: 0.7268 (mm110) REVERT: L 80 GLU cc_start: 0.8575 (tt0) cc_final: 0.8069 (tt0) REVERT: L 82 GLU cc_start: 0.8307 (pm20) cc_final: 0.7229 (pm20) outliers start: 16 outliers final: 12 residues processed: 67 average time/residue: 0.1499 time to fit residues: 12.8155 Evaluate side-chains 69 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 422 ASN Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 571 ASP 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 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 39 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 0.0170 chunk 46 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1981 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= 0.206 Angle : 0.627 10.403 5301 Z= 0.308 Chirality : 0.044 0.168 587 Planarity : 0.004 0.031 679 Dihedral : 7.426 55.553 585 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 4.31 % Allowed : 14.11 % Favored : 81.58 % 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: -0.48 (0.40), residues: 477 helix: -3.13 (0.82), residues: 27 sheet: 1.16 (0.44), residues: 155 loop : -0.90 (0.37), residues: 295 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 0.009 0.001 PHE C 559 TYR 0.023 0.001 TYR C 369 ARG 0.010 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 72 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 54 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: C 358 ILE cc_start: 0.8524 (mm) cc_final: 0.8289 (mt) REVERT: C 365 TYR cc_start: 0.5624 (p90) cc_final: 0.5349 (p90) REVERT: C 559 PHE cc_start: 0.3050 (OUTLIER) cc_final: 0.1536 (m-80) REVERT: C 563 GLN cc_start: 0.8238 (mt0) cc_final: 0.7268 (mm110) REVERT: L 80 GLU cc_start: 0.8602 (tt0) cc_final: 0.8189 (tt0) outliers start: 18 outliers final: 15 residues processed: 65 average time/residue: 0.1475 time to fit residues: 12.3708 Evaluate side-chains 68 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 52 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 422 ASN Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 571 ASP 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 22 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3908 Z= 0.222 Angle : 0.633 10.257 5301 Z= 0.311 Chirality : 0.045 0.177 587 Planarity : 0.004 0.034 679 Dihedral : 7.238 52.686 585 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.83 % Allowed : 15.31 % Favored : 80.86 % 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: -0.48 (0.40), residues: 477 helix: -3.11 (0.75), residues: 33 sheet: 1.17 (0.44), residues: 155 loop : -0.84 (0.37), residues: 289 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 0.009 0.001 PHE C 392 TYR 0.023 0.001 TYR C 369 ARG 0.010 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 70 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 54 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: C 358 ILE cc_start: 0.8525 (mm) cc_final: 0.8291 (mt) REVERT: C 365 TYR cc_start: 0.5642 (p90) cc_final: 0.5368 (p90) REVERT: C 559 PHE cc_start: 0.3103 (OUTLIER) cc_final: 0.1526 (m-80) REVERT: C 563 GLN cc_start: 0.8244 (mt0) cc_final: 0.7321 (mm110) REVERT: L 80 GLU cc_start: 0.8600 (tt0) cc_final: 0.8191 (tt0) outliers start: 16 outliers final: 14 residues processed: 64 average time/residue: 0.1509 time to fit residues: 12.4947 Evaluate side-chains 67 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 52 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 422 ASN Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 571 ASP 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 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: 0.8980 chunk 32 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.074918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.060019 restraints weight = 12829.153| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.81 r_work: 0.3075 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3908 Z= 0.234 Angle : 0.636 10.173 5301 Z= 0.313 Chirality : 0.045 0.187 587 Planarity : 0.004 0.033 679 Dihedral : 7.188 52.846 585 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 3.83 % Allowed : 15.31 % Favored : 80.86 % 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 (0.40), residues: 477 helix: -3.14 (0.74), residues: 33 sheet: 1.15 (0.44), residues: 155 loop : -0.86 (0.37), residues: 289 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 0.009 0.001 PHE C 559 TYR 0.023 0.001 TYR C 369 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: 1347.23 seconds wall clock time: 24 minutes 58.84 seconds (1498.84 seconds total)