Starting phenix.real_space_refine on Thu Nov 14 08:47:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zhg_60102/11_2024/8zhg_60102.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zhg_60102/11_2024/8zhg_60102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zhg_60102/11_2024/8zhg_60102.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zhg_60102/11_2024/8zhg_60102.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zhg_60102/11_2024/8zhg_60102.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zhg_60102/11_2024/8zhg_60102.cif" } resolution = 3.51 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= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2345 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2100 2.51 5 N 556 2.21 5 O 655 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3326 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1552 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 926 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 820 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.70, per 1000 atoms: 0.81 Number of scatterers: 3326 At special positions: 0 Unit cell: (71.1776, 88.972, 79.3904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 655 8.00 N 556 7.00 C 2100 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 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 22 " - pdb=" SG CYS L 91 " 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 A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN C 343 " Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 392.3 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 7 sheets defined 8.7% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.895A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.611A pdb=" N LYS C 386 " --> pdb=" O SER C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 removed outlier: 3.567A pdb=" N ILE C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA C 411 " --> pdb=" O VAL C 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 406 through 411' Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.926A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.625A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.509A pdb=" N ASP L 85 " --> pdb=" O LYS L 82 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU L 86 " --> pdb=" O THR L 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 82 through 86' Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.817A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL C 433 " --> pdb=" O PHE C 377 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE C 377 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA C 435 " --> pdb=" O SER C 375 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 17 through 23 Processing sheet with id=AA3, first strand: chain 'H' and resid 58 through 59 removed outlier: 4.874A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN H 39 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N CYS H 96 " --> pdb=" O TRP H 110 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N TRP H 110 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ARG H 98 " --> pdb=" O ASP H 108 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 58 through 59 removed outlier: 4.874A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN H 39 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR H 114 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA6, first strand: chain 'L' and resid 46 through 49 removed outlier: 3.965A pdb=" N VAL L 48 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR L 90 " --> pdb=" O TYR L 37 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN L 39 " --> pdb=" O ASP L 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 46 through 49 removed outlier: 3.965A pdb=" N VAL L 48 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR L 90 " --> pdb=" O TYR L 37 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN L 39 " --> pdb=" O ASP L 88 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR L 89 " --> pdb=" O THR L 105 " (cutoff:3.500A) 88 hydrogen bonds defined for protein. 216 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.83 Time building geometry restraints manager: 0.92 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: 1070 1.35 - 1.47: 932 1.47 - 1.59: 1391 1.59 - 1.71: 0 1.71 - 1.84: 18 Bond restraints: 3411 Sorted by residual: bond pdb=" N TYR C 473 " pdb=" CA TYR C 473 " ideal model delta sigma weight residual 1.455 1.484 -0.030 1.27e-02 6.20e+03 5.42e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.73e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" CB GLU L 86 " pdb=" CG GLU L 86 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.11e+00 bond pdb=" C TYR C 473 " pdb=" O TYR C 473 " ideal model delta sigma weight residual 1.234 1.251 -0.017 1.27e-02 6.20e+03 1.88e+00 ... (remaining 3406 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 4447 1.40 - 2.80: 153 2.80 - 4.20: 26 4.20 - 5.61: 8 5.61 - 7.01: 5 Bond angle restraints: 4639 Sorted by residual: angle pdb=" CB GLU L 86 " pdb=" CG GLU L 86 " pdb=" CD GLU L 86 " ideal model delta sigma weight residual 112.60 118.01 -5.41 1.70e+00 3.46e-01 1.01e+01 angle pdb=" CA LYS H 43 " pdb=" CB LYS H 43 " pdb=" CG LYS H 43 " ideal model delta sigma weight residual 114.10 120.30 -6.20 2.00e+00 2.50e-01 9.62e+00 angle pdb=" C CYS C 480 " pdb=" N ASN C 481 " pdb=" CA ASN C 481 " ideal model delta sigma weight residual 121.54 127.17 -5.63 1.91e+00 2.74e-01 8.68e+00 angle pdb=" CA GLU L 86 " pdb=" CB GLU L 86 " pdb=" CG GLU L 86 " ideal model delta sigma weight residual 114.10 119.36 -5.26 2.00e+00 2.50e-01 6.92e+00 angle pdb=" CA LYS L 16 " pdb=" CB LYS L 16 " pdb=" CG LYS L 16 " ideal model delta sigma weight residual 114.10 119.22 -5.12 2.00e+00 2.50e-01 6.55e+00 ... (remaining 4634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 1709 17.23 - 34.45: 227 34.45 - 51.68: 67 51.68 - 68.91: 13 68.91 - 86.14: 7 Dihedral angle restraints: 2023 sinusoidal: 803 harmonic: 1220 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 60.96 32.04 1 1.00e+01 1.00e-02 1.46e+01 dihedral pdb=" CA ASP L 68 " pdb=" CB ASP L 68 " pdb=" CG ASP L 68 " pdb=" OD1 ASP L 68 " ideal model delta sinusoidal sigma weight residual -30.00 -89.46 59.46 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 66.49 26.51 1 1.00e+01 1.00e-02 1.01e+01 ... (remaining 2020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 303 0.033 - 0.067: 136 0.067 - 0.100: 36 0.100 - 0.133: 20 0.133 - 0.166: 2 Chirality restraints: 497 Sorted by residual: chirality pdb=" CG LEU H 86 " pdb=" CB LEU H 86 " pdb=" CD1 LEU H 86 " pdb=" CD2 LEU H 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CG LEU C 452 " pdb=" CB LEU C 452 " pdb=" CD1 LEU C 452 " pdb=" CD2 LEU C 452 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" CB ILE L 49 " pdb=" CA ILE L 49 " pdb=" CG1 ILE L 49 " pdb=" CG2 ILE L 49 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 494 not shown) Planarity restraints: 603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 13 " -0.059 5.00e-02 4.00e+02 8.98e-02 1.29e+01 pdb=" N PRO L 14 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO L 14 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO L 14 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 462 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO C 463 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO C 521 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " 0.019 5.00e-02 4.00e+02 ... (remaining 600 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 888 2.80 - 3.32: 2682 3.32 - 3.85: 5331 3.85 - 4.37: 5856 4.37 - 4.90: 10330 Nonbonded interactions: 25087 Sorted by model distance: nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.273 3.040 nonbonded pdb=" OG1 THR C 415 " pdb=" OD1 ASP C 420 " model vdw 2.323 3.040 nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.339 3.040 nonbonded pdb=" OG1 THR C 430 " pdb=" O PHE C 515 " model vdw 2.347 3.040 nonbonded pdb=" OE1 GLU H 57 " pdb=" OH TYR H 59 " model vdw 2.353 3.040 ... (remaining 25082 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.620 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: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 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 : 0.003 0.051 3411 Z= 0.221 Angle : 0.657 7.007 4639 Z= 0.335 Chirality : 0.044 0.166 497 Planarity : 0.007 0.090 602 Dihedral : 17.545 86.137 1235 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.11 % Allowed : 32.69 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.40), residues: 419 helix: -4.79 (0.32), residues: 19 sheet: 1.06 (0.51), residues: 119 loop : -1.75 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 110 HIS 0.002 0.001 HIS L 8 PHE 0.009 0.001 PHE C 456 TYR 0.019 0.001 TYR C 453 ARG 0.009 0.001 ARG L 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.363 Fit side-chains REVERT: C 465 GLU cc_start: 0.6576 (mt-10) cc_final: 0.6116 (mt-10) REVERT: H 115 LEU cc_start: 0.8755 (tp) cc_final: 0.8505 (tt) outliers start: 4 outliers final: 2 residues processed: 50 average time/residue: 0.2252 time to fit residues: 13.2274 Evaluate side-chains 46 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain H residue 77 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.0170 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.0010 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 overall best weight: 0.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 437 ASN C 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3411 Z= 0.224 Angle : 0.538 4.743 4639 Z= 0.287 Chirality : 0.043 0.143 497 Planarity : 0.006 0.070 602 Dihedral : 4.481 41.053 514 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.99 % Allowed : 26.87 % Favored : 68.14 % 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: -1.47 (0.39), residues: 419 helix: -4.54 (0.50), residues: 18 sheet: 0.54 (0.47), residues: 131 loop : -1.60 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 436 HIS 0.001 0.000 HIS L 8 PHE 0.013 0.001 PHE C 429 TYR 0.016 0.001 TYR C 495 ARG 0.007 0.001 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.426 Fit side-chains REVERT: C 346 ARG cc_start: 0.7330 (mtp85) cc_final: 0.6939 (mtp85) REVERT: L 10 VAL cc_start: 0.4422 (OUTLIER) cc_final: 0.4216 (p) outliers start: 18 outliers final: 11 residues processed: 58 average time/residue: 0.1589 time to fit residues: 11.4209 Evaluate side-chains 53 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 59 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 36 optimal weight: 0.0870 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 overall best weight: 0.4156 ------------------------------------------------------------------------------- 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: 0.7346 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3411 Z= 0.202 Angle : 0.537 4.614 4639 Z= 0.282 Chirality : 0.042 0.133 497 Planarity : 0.005 0.062 602 Dihedral : 3.826 15.328 510 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.99 % Allowed : 28.53 % Favored : 66.48 % 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: -1.27 (0.39), residues: 419 helix: -4.52 (0.54), residues: 18 sheet: 0.80 (0.48), residues: 129 loop : -1.51 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.002 0.001 HIS L 8 PHE 0.016 0.001 PHE C 429 TYR 0.018 0.001 TYR C 495 ARG 0.003 0.001 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.348 Fit side-chains REVERT: C 346 ARG cc_start: 0.7496 (mtp85) cc_final: 0.7070 (mtp85) REVERT: C 429 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.7210 (t80) REVERT: C 495 TYR cc_start: 0.7925 (OUTLIER) cc_final: 0.6438 (t80) REVERT: C 516 GLU cc_start: 0.7782 (pm20) cc_final: 0.7078 (pt0) REVERT: L 97 SER cc_start: 0.7520 (m) cc_final: 0.7153 (p) outliers start: 18 outliers final: 14 residues processed: 58 average time/residue: 0.2014 time to fit residues: 13.8357 Evaluate side-chains 60 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 37 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 437 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3411 Z= 0.216 Angle : 0.542 5.005 4639 Z= 0.287 Chirality : 0.043 0.133 497 Planarity : 0.005 0.060 602 Dihedral : 3.899 13.617 510 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 5.26 % Allowed : 28.81 % Favored : 65.93 % 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: -1.25 (0.40), residues: 419 helix: -4.52 (0.53), residues: 18 sheet: 0.82 (0.49), residues: 130 loop : -1.50 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 PHE 0.017 0.002 PHE C 429 TYR 0.022 0.001 TYR C 495 ARG 0.006 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.344 Fit side-chains REVERT: C 346 ARG cc_start: 0.7522 (mtp85) cc_final: 0.7131 (mtp85) REVERT: C 430 THR cc_start: 0.8532 (p) cc_final: 0.8273 (p) REVERT: C 495 TYR cc_start: 0.7740 (OUTLIER) cc_final: 0.6196 (t80) REVERT: C 516 GLU cc_start: 0.7750 (pm20) cc_final: 0.7214 (pt0) REVERT: L 97 SER cc_start: 0.7822 (m) cc_final: 0.7433 (p) outliers start: 19 outliers final: 15 residues processed: 60 average time/residue: 0.1993 time to fit residues: 14.3937 Evaluate side-chains 57 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 29 optimal weight: 0.0870 chunk 16 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 35 optimal weight: 0.0370 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3411 Z= 0.200 Angle : 0.533 4.998 4639 Z= 0.282 Chirality : 0.043 0.137 497 Planarity : 0.005 0.057 602 Dihedral : 3.967 19.095 510 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 6.37 % Allowed : 26.87 % Favored : 66.76 % 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: -1.24 (0.40), residues: 419 helix: -4.43 (0.59), residues: 18 sheet: 0.85 (0.48), residues: 129 loop : -1.51 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.001 0.000 HIS L 8 PHE 0.019 0.001 PHE C 429 TYR 0.021 0.001 TYR C 495 ARG 0.008 0.001 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 38 time to evaluate : 0.512 Fit side-chains REVERT: C 334 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.7319 (p0) REVERT: C 346 ARG cc_start: 0.7517 (mtp85) cc_final: 0.7133 (mtp85) REVERT: C 495 TYR cc_start: 0.7701 (OUTLIER) cc_final: 0.6181 (t80) REVERT: C 516 GLU cc_start: 0.7721 (pm20) cc_final: 0.7328 (pt0) outliers start: 23 outliers final: 18 residues processed: 57 average time/residue: 0.2112 time to fit residues: 14.4213 Evaluate side-chains 56 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 36 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.0010 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.1980 chunk 20 optimal weight: 0.3980 chunk 38 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3411 Z= 0.154 Angle : 0.515 6.547 4639 Z= 0.268 Chirality : 0.042 0.134 497 Planarity : 0.005 0.053 602 Dihedral : 3.840 19.127 510 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 6.09 % Allowed : 26.59 % Favored : 67.31 % 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: -1.09 (0.40), residues: 419 helix: -4.32 (0.60), residues: 18 sheet: 0.89 (0.48), residues: 129 loop : -1.36 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.000 0.000 HIS L 8 PHE 0.016 0.001 PHE C 429 TYR 0.016 0.001 TYR C 495 ARG 0.005 0.001 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 38 time to evaluate : 0.379 Fit side-chains REVERT: C 346 ARG cc_start: 0.7438 (mtp85) cc_final: 0.7035 (mtp85) REVERT: C 454 ARG cc_start: 0.8382 (ttm-80) cc_final: 0.8175 (ttm-80) REVERT: C 495 TYR cc_start: 0.7705 (OUTLIER) cc_final: 0.6450 (t80) REVERT: C 516 GLU cc_start: 0.7770 (pm20) cc_final: 0.7401 (pt0) outliers start: 22 outliers final: 19 residues processed: 57 average time/residue: 0.2107 time to fit residues: 14.7000 Evaluate side-chains 56 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 36 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 0.0970 chunk 33 optimal weight: 0.0030 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 25 optimal weight: 0.2980 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3411 Z= 0.168 Angle : 0.516 5.735 4639 Z= 0.270 Chirality : 0.042 0.136 497 Planarity : 0.005 0.051 602 Dihedral : 3.843 18.498 510 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 6.93 % Allowed : 25.48 % Favored : 67.59 % 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: -1.01 (0.40), residues: 419 helix: -4.25 (0.61), residues: 18 sheet: 0.94 (0.48), residues: 129 loop : -1.31 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.001 0.000 HIS L 8 PHE 0.017 0.001 PHE C 429 TYR 0.019 0.001 TYR C 495 ARG 0.005 0.001 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 40 time to evaluate : 0.368 Fit side-chains REVERT: C 334 ASN cc_start: 0.7352 (OUTLIER) cc_final: 0.6999 (p0) REVERT: C 346 ARG cc_start: 0.7451 (mtp85) cc_final: 0.7040 (mtp85) REVERT: C 430 THR cc_start: 0.8512 (p) cc_final: 0.8279 (p) REVERT: C 495 TYR cc_start: 0.7627 (OUTLIER) cc_final: 0.6349 (t80) REVERT: C 516 GLU cc_start: 0.7820 (pm20) cc_final: 0.7479 (pt0) outliers start: 25 outliers final: 20 residues processed: 62 average time/residue: 0.1804 time to fit residues: 13.5687 Evaluate side-chains 59 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 37 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.0030 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.0770 chunk 28 optimal weight: 0.8980 overall best weight: 0.4948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3411 Z= 0.215 Angle : 0.548 5.650 4639 Z= 0.287 Chirality : 0.043 0.139 497 Planarity : 0.005 0.053 602 Dihedral : 4.043 17.903 510 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 7.20 % Allowed : 24.65 % Favored : 68.14 % 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: -1.14 (0.40), residues: 419 helix: -4.23 (0.55), residues: 19 sheet: 0.68 (0.47), residues: 135 loop : -1.34 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.001 0.000 HIS L 8 PHE 0.020 0.001 PHE C 429 TYR 0.024 0.001 TYR C 495 ARG 0.006 0.001 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 40 time to evaluate : 0.445 Fit side-chains REVERT: C 334 ASN cc_start: 0.7555 (OUTLIER) cc_final: 0.7075 (p0) REVERT: C 346 ARG cc_start: 0.7456 (mtp85) cc_final: 0.7140 (mtp85) REVERT: C 394 ASN cc_start: 0.7564 (m-40) cc_final: 0.7331 (m-40) REVERT: C 430 THR cc_start: 0.8670 (p) cc_final: 0.8469 (p) REVERT: C 490 PHE cc_start: 0.7814 (t80) cc_final: 0.7599 (t80) REVERT: C 495 TYR cc_start: 0.7716 (OUTLIER) cc_final: 0.6058 (t80) REVERT: C 516 GLU cc_start: 0.7992 (pm20) cc_final: 0.7647 (pt0) outliers start: 26 outliers final: 19 residues processed: 61 average time/residue: 0.2018 time to fit residues: 14.9694 Evaluate side-chains 59 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 38 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7508 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3411 Z= 0.276 Angle : 0.589 6.423 4639 Z= 0.310 Chirality : 0.044 0.142 497 Planarity : 0.005 0.056 602 Dihedral : 4.323 17.300 510 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 5.82 % Allowed : 26.32 % Favored : 67.87 % 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: -1.27 (0.40), residues: 419 helix: -4.19 (0.55), residues: 19 sheet: 0.54 (0.46), residues: 135 loop : -1.41 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.002 0.001 HIS L 8 PHE 0.024 0.002 PHE C 429 TYR 0.030 0.002 TYR C 495 ARG 0.005 0.001 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 39 time to evaluate : 0.374 Fit side-chains REVERT: C 346 ARG cc_start: 0.7430 (mtp85) cc_final: 0.7125 (mtp85) REVERT: C 430 THR cc_start: 0.8815 (p) cc_final: 0.8602 (p) REVERT: C 442 ASP cc_start: 0.8099 (m-30) cc_final: 0.7724 (m-30) REVERT: C 495 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.6246 (t80) REVERT: C 516 GLU cc_start: 0.8007 (pm20) cc_final: 0.7699 (pt0) outliers start: 21 outliers final: 18 residues processed: 55 average time/residue: 0.1791 time to fit residues: 11.9968 Evaluate side-chains 58 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 39 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.0470 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.0770 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.4436 ------------------------------------------------------------------------------- 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: 0.7477 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3411 Z= 0.202 Angle : 0.548 5.942 4639 Z= 0.288 Chirality : 0.043 0.142 497 Planarity : 0.005 0.055 602 Dihedral : 4.136 16.762 510 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 5.26 % Allowed : 26.87 % Favored : 67.87 % 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: -1.21 (0.40), residues: 419 helix: -4.19 (0.58), residues: 19 sheet: 0.54 (0.47), residues: 135 loop : -1.33 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.001 0.000 HIS L 8 PHE 0.021 0.001 PHE C 429 TYR 0.022 0.001 TYR C 495 ARG 0.004 0.001 ARG C 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 38 time to evaluate : 0.392 Fit side-chains REVERT: C 346 ARG cc_start: 0.7459 (mtp85) cc_final: 0.7163 (mtp85) REVERT: C 490 PHE cc_start: 0.7778 (t80) cc_final: 0.7577 (t80) REVERT: C 495 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.6198 (t80) REVERT: C 516 GLU cc_start: 0.7898 (pm20) cc_final: 0.7583 (pt0) outliers start: 19 outliers final: 17 residues processed: 52 average time/residue: 0.2072 time to fit residues: 13.0586 Evaluate side-chains 56 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 38 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.2980 chunk 1 optimal weight: 0.3980 chunk 23 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.0770 chunk 16 optimal weight: 0.0050 chunk 15 optimal weight: 0.0370 chunk 40 optimal weight: 1.9990 overall best weight: 0.1230 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.164990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.132043 restraints weight = 4035.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.134749 restraints weight = 3787.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.135837 restraints weight = 2559.114| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3411 Z= 0.134 Angle : 0.499 5.256 4639 Z= 0.262 Chirality : 0.041 0.136 497 Planarity : 0.004 0.051 602 Dihedral : 3.740 15.965 510 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.71 % Allowed : 27.42 % Favored : 67.87 % 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: -0.90 (0.41), residues: 419 helix: -4.10 (0.63), residues: 19 sheet: 0.75 (0.47), residues: 137 loop : -1.12 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.001 0.000 HIS C 519 PHE 0.016 0.001 PHE C 429 TYR 0.011 0.001 TYR H 60 ARG 0.004 0.001 ARG C 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1312.99 seconds wall clock time: 24 minutes 51.16 seconds (1491.16 seconds total)