Starting phenix.real_space_refine on Tue Feb 13 05:54:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru4_24696/02_2024/7ru4_24696.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru4_24696/02_2024/7ru4_24696.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/7ru4_24696/02_2024/7ru4_24696.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru4_24696/02_2024/7ru4_24696.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru4_24696/02_2024/7ru4_24696.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru4_24696/02_2024/7ru4_24696.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= -0.001 sd= 0.016 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 14 5.16 5 C 2151 2.51 5 N 564 2.21 5 O 653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 3382 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 894 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 826 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1610 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 1 Chain: "B" 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 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.08, per 1000 atoms: 0.62 Number of scatterers: 3382 At special positions: 0 Unit cell: (64.89, 99.91, 84.46, 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 14 16.00 O 653 8.00 N 564 7.00 C 2151 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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 B 1 " - " NAG B 2 " BETA1-6 " NAG B 1 " - " FUC B 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG B 1 " - " ASN A 343 " Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 668.5 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 9 sheets defined 15.0% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.799A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.899A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.233A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.886A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.208A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 9 through 11 removed outlier: 4.048A pdb=" N ALA H 9 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR H 110 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 9 through 11 removed outlier: 4.048A pdb=" N ALA H 9 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR H 110 " --> pdb=" O ALA H 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.482A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.500A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 127 hydrogen bonds defined for protein. 297 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: 0.98 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 949 1.33 - 1.47: 1110 1.47 - 1.61: 1385 1.61 - 1.74: 4 1.74 - 1.88: 16 Bond restraints: 3464 Sorted by residual: bond pdb=" CB ILE A 326 " pdb=" CG1 ILE A 326 " ideal model delta sigma weight residual 1.530 1.679 -0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" CG GLN L 6 " pdb=" CD GLN L 6 " ideal model delta sigma weight residual 1.516 1.384 0.132 2.50e-02 1.60e+03 2.79e+01 bond pdb=" CB TYR L 87 " pdb=" CG TYR L 87 " ideal model delta sigma weight residual 1.512 1.397 0.115 2.20e-02 2.07e+03 2.75e+01 bond pdb=" CB TYR L 36 " pdb=" CG TYR L 36 " ideal model delta sigma weight residual 1.512 1.398 0.114 2.20e-02 2.07e+03 2.67e+01 bond pdb=" CB ILE A 472 " pdb=" CG2 ILE A 472 " ideal model delta sigma weight residual 1.521 1.363 0.158 3.30e-02 9.18e+02 2.29e+01 ... (remaining 3459 not shown) Histogram of bond angle deviations from ideal: 101.15 - 107.78: 260 107.78 - 114.42: 1731 114.42 - 121.06: 1660 121.06 - 127.70: 1025 127.70 - 134.33: 30 Bond angle restraints: 4706 Sorted by residual: angle pdb=" N ARG L 61 " pdb=" CA ARG L 61 " pdb=" C ARG L 61 " ideal model delta sigma weight residual 114.56 101.68 12.88 1.27e+00 6.20e-01 1.03e+02 angle pdb=" N ALA A 520 " pdb=" CA ALA A 520 " pdb=" C ALA A 520 " ideal model delta sigma weight residual 108.13 117.09 -8.96 9.00e-01 1.23e+00 9.91e+01 angle pdb=" N LEU H 54 " pdb=" CA LEU H 54 " pdb=" C LEU H 54 " ideal model delta sigma weight residual 113.97 102.00 11.97 1.28e+00 6.10e-01 8.75e+01 angle pdb=" N GLN A 474 " pdb=" CA GLN A 474 " pdb=" C GLN A 474 " ideal model delta sigma weight residual 110.55 122.38 -11.83 1.35e+00 5.49e-01 7.68e+01 angle pdb=" N PHE L 98 " pdb=" CA PHE L 98 " pdb=" C PHE L 98 " ideal model delta sigma weight residual 113.30 124.82 -11.52 1.34e+00 5.57e-01 7.39e+01 ... (remaining 4701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.72: 1998 14.72 - 29.45: 69 29.45 - 44.17: 15 44.17 - 58.90: 13 58.90 - 73.62: 4 Dihedral angle restraints: 2099 sinusoidal: 864 harmonic: 1235 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 138.11 -45.11 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 64.13 28.87 1 1.00e+01 1.00e-02 1.19e+01 dihedral pdb=" SG CYS A 391 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " pdb=" CA CYS A 525 " ideal model delta sinusoidal sigma weight residual 79.00 23.24 55.76 1 2.00e+01 2.50e-03 1.05e+01 ... (remaining 2096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 322 0.087 - 0.173: 141 0.173 - 0.260: 46 0.260 - 0.346: 11 0.346 - 0.433: 6 Chirality restraints: 526 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.08e+02 chirality pdb=" C1 FUC B 3 " pdb=" O6 NAG B 1 " pdb=" C2 FUC B 3 " pdb=" O5 FUC B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.98e+01 chirality pdb=" C2 NAG B 2 " pdb=" C1 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" N2 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.92 0.43 2.00e-01 2.50e+01 4.68e+00 ... (remaining 523 not shown) Planarity restraints: 599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " -0.057 2.00e-02 2.50e+03 2.67e-02 1.78e+01 pdb=" CG TRP H 47 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " 0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " 0.026 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " -0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 32 " -0.056 2.00e-02 2.50e+03 2.94e-02 1.73e+01 pdb=" CG TYR L 32 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR L 32 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR L 32 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR L 32 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR L 32 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR L 32 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR L 32 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 478 " 0.018 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C THR A 478 " -0.060 2.00e-02 2.50e+03 pdb=" O THR A 478 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO A 479 " 0.020 2.00e-02 2.50e+03 ... (remaining 596 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1243 2.87 - 3.38: 2954 3.38 - 3.88: 5675 3.88 - 4.39: 6717 4.39 - 4.90: 10862 Nonbonded interactions: 27451 Sorted by model distance: nonbonded pdb=" OE1 GLU A 340 " pdb=" NZ LYS A 356 " model vdw 2.362 2.520 nonbonded pdb=" N LEU H 54 " pdb=" N ASP H 55 " model vdw 2.363 2.560 nonbonded pdb=" N ARG L 61 " pdb=" N PHE L 62 " model vdw 2.377 2.560 nonbonded pdb=" N PRO A 426 " pdb=" O PRO A 426 " model vdw 2.440 2.496 nonbonded pdb=" N GLN H 97 " pdb=" O GLN H 97 " model vdw 2.463 2.496 ... (remaining 27446 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: 3.440 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: 17.820 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 13.990 Find NCS groups from input model: 0.080 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 38.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 0.023 0.158 3464 Z= 1.507 Angle : 1.894 12.879 4706 Z= 1.262 Chirality : 0.113 0.433 526 Planarity : 0.008 0.035 597 Dihedral : 9.651 73.619 1295 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.55 % Allowed : 1.10 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.06 (0.40), residues: 420 helix: -3.40 (0.59), residues: 31 sheet: 1.34 (0.44), residues: 150 loop : -0.30 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.010 TRP H 47 HIS 0.003 0.002 HIS L 90 PHE 0.026 0.005 PHE A 374 TYR 0.056 0.008 TYR L 32 ARG 0.005 0.001 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 120 time to evaluate : 0.343 Fit side-chains REVERT: H 89 VAL cc_start: 0.9153 (t) cc_final: 0.8894 (p) REVERT: A 332 ILE cc_start: 0.8865 (mt) cc_final: 0.8380 (mt) REVERT: A 336 CYS cc_start: 0.6290 (m) cc_final: 0.5884 (m) REVERT: A 360 ASN cc_start: 0.8823 (t0) cc_final: 0.8398 (t0) REVERT: A 453 TYR cc_start: 0.5598 (m-80) cc_final: 0.5330 (m-80) REVERT: A 458 LYS cc_start: 0.7751 (pttt) cc_final: 0.7151 (mmtm) outliers start: 2 outliers final: 0 residues processed: 122 average time/residue: 0.2354 time to fit residues: 32.5604 Evaluate side-chains 75 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 97 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3464 Z= 0.282 Angle : 0.750 10.824 4706 Z= 0.394 Chirality : 0.050 0.217 526 Planarity : 0.005 0.038 597 Dihedral : 6.013 34.250 549 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.84 % Allowed : 8.49 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.21 (0.40), residues: 420 helix: -1.74 (1.21), residues: 25 sheet: 0.88 (0.42), residues: 149 loop : -0.60 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 47 HIS 0.002 0.001 HIS L 90 PHE 0.009 0.002 PHE L 62 TYR 0.022 0.002 TYR A 495 ARG 0.006 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.356 Fit side-chains REVERT: H 4 LEU cc_start: 0.8050 (mt) cc_final: 0.7836 (mm) REVERT: H 100 LEU cc_start: 0.9239 (mt) cc_final: 0.8903 (mt) REVERT: L 21 LEU cc_start: 0.8911 (mm) cc_final: 0.8640 (mp) REVERT: A 328 ARG cc_start: 0.7428 (tpt90) cc_final: 0.4734 (pmt-80) REVERT: A 356 LYS cc_start: 0.8541 (tttt) cc_final: 0.7438 (tttt) REVERT: A 386 LYS cc_start: 0.4647 (mttt) cc_final: 0.4416 (mttt) REVERT: A 420 ASP cc_start: 0.6488 (m-30) cc_final: 0.5695 (t0) REVERT: A 458 LYS cc_start: 0.7649 (pttt) cc_final: 0.7001 (mmpt) REVERT: A 460 ASN cc_start: 0.6791 (m-40) cc_final: 0.6021 (m-40) outliers start: 14 outliers final: 7 residues processed: 94 average time/residue: 0.1602 time to fit residues: 18.1898 Evaluate side-chains 79 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 398 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.0040 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 97 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3464 Z= 0.226 Angle : 0.643 7.448 4706 Z= 0.333 Chirality : 0.047 0.235 526 Planarity : 0.005 0.045 597 Dihedral : 5.679 41.687 549 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.84 % Allowed : 12.33 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.17 (0.40), residues: 420 helix: -1.89 (1.12), residues: 25 sheet: 1.00 (0.43), residues: 151 loop : -0.65 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.001 0.001 HIS L 90 PHE 0.018 0.001 PHE A 497 TYR 0.016 0.002 TYR L 91 ARG 0.005 0.001 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.398 Fit side-chains REVERT: H 110 THR cc_start: 0.8275 (p) cc_final: 0.8050 (p) REVERT: L 21 LEU cc_start: 0.8938 (mm) cc_final: 0.8650 (mp) REVERT: L 49 TYR cc_start: 0.9058 (p90) cc_final: 0.8848 (p90) REVERT: L 81 GLU cc_start: 0.7979 (pm20) cc_final: 0.7665 (pm20) REVERT: A 328 ARG cc_start: 0.7412 (tpt90) cc_final: 0.4813 (pmt-80) REVERT: A 420 ASP cc_start: 0.6554 (m-30) cc_final: 0.5822 (t0) REVERT: A 458 LYS cc_start: 0.7641 (pttt) cc_final: 0.7000 (mmtt) REVERT: A 460 ASN cc_start: 0.6972 (m-40) cc_final: 0.6225 (m-40) outliers start: 14 outliers final: 8 residues processed: 88 average time/residue: 0.1654 time to fit residues: 17.5623 Evaluate side-chains 79 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 97 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 398 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 4 optimal weight: 0.2980 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 0.0970 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 3464 Z= 0.209 Angle : 0.629 7.834 4706 Z= 0.320 Chirality : 0.047 0.191 526 Planarity : 0.005 0.046 597 Dihedral : 5.483 39.219 549 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.56 % Allowed : 12.05 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.21 (0.40), residues: 420 helix: -2.14 (1.02), residues: 26 sheet: 1.01 (0.42), residues: 153 loop : -0.67 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 98 HIS 0.001 0.001 HIS L 90 PHE 0.005 0.001 PHE A 497 TYR 0.017 0.002 TYR A 369 ARG 0.005 0.001 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: H 110 THR cc_start: 0.8148 (p) cc_final: 0.7922 (p) REVERT: L 21 LEU cc_start: 0.8916 (mm) cc_final: 0.8634 (mp) REVERT: L 81 GLU cc_start: 0.7990 (pm20) cc_final: 0.7767 (pm20) REVERT: L 87 TYR cc_start: 0.6384 (p90) cc_final: 0.6132 (p90) REVERT: A 328 ARG cc_start: 0.7442 (tpt90) cc_final: 0.4893 (pmt-80) REVERT: A 420 ASP cc_start: 0.6561 (m-30) cc_final: 0.5793 (t0) REVERT: A 458 LYS cc_start: 0.7579 (pttt) cc_final: 0.6920 (mmtt) REVERT: A 460 ASN cc_start: 0.7053 (m-40) cc_final: 0.6348 (m-40) outliers start: 13 outliers final: 11 residues processed: 85 average time/residue: 0.1624 time to fit residues: 16.9151 Evaluate side-chains 80 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 0.0170 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3464 Z= 0.255 Angle : 0.633 7.548 4706 Z= 0.323 Chirality : 0.047 0.216 526 Planarity : 0.005 0.043 597 Dihedral : 5.711 46.650 549 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.38 % Allowed : 12.88 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.39 (0.40), residues: 420 helix: -2.22 (1.01), residues: 26 sheet: 1.00 (0.42), residues: 152 loop : -0.89 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 98 HIS 0.001 0.001 HIS L 90 PHE 0.008 0.001 PHE A 486 TYR 0.041 0.002 TYR A 453 ARG 0.003 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: H 110 THR cc_start: 0.8173 (p) cc_final: 0.7942 (p) REVERT: A 328 ARG cc_start: 0.7485 (tpt90) cc_final: 0.4877 (pmt-80) REVERT: A 360 ASN cc_start: 0.8885 (t0) cc_final: 0.8664 (t0) REVERT: A 392 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7360 (m-80) REVERT: A 420 ASP cc_start: 0.6506 (m-30) cc_final: 0.5714 (t0) REVERT: A 458 LYS cc_start: 0.7562 (pttt) cc_final: 0.6895 (mmtt) REVERT: A 460 ASN cc_start: 0.7002 (m-40) cc_final: 0.6286 (m-40) outliers start: 16 outliers final: 10 residues processed: 81 average time/residue: 0.1751 time to fit residues: 17.1759 Evaluate side-chains 84 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.0570 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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: 0.7981 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3464 Z= 0.221 Angle : 0.627 7.420 4706 Z= 0.320 Chirality : 0.047 0.202 526 Planarity : 0.005 0.042 597 Dihedral : 5.485 38.804 549 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.38 % Allowed : 13.70 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 420 helix: -2.23 (0.99), residues: 26 sheet: 1.08 (0.42), residues: 152 loop : -0.97 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 98 HIS 0.001 0.001 HIS L 90 PHE 0.009 0.001 PHE L 83 TYR 0.030 0.002 TYR A 453 ARG 0.003 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 77 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: H 110 THR cc_start: 0.8149 (p) cc_final: 0.7908 (p) REVERT: L 21 LEU cc_start: 0.8838 (mm) cc_final: 0.8532 (mp) REVERT: A 328 ARG cc_start: 0.7503 (tpt90) cc_final: 0.4931 (pmt-80) REVERT: A 360 ASN cc_start: 0.8876 (t0) cc_final: 0.8662 (t0) REVERT: A 392 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7164 (m-80) REVERT: A 420 ASP cc_start: 0.6602 (m-30) cc_final: 0.5762 (t0) REVERT: A 458 LYS cc_start: 0.7486 (pttt) cc_final: 0.6794 (mmtt) REVERT: A 460 ASN cc_start: 0.7041 (m-40) cc_final: 0.6334 (m-40) outliers start: 16 outliers final: 11 residues processed: 83 average time/residue: 0.1798 time to fit residues: 17.8700 Evaluate side-chains 83 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 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: 0.8002 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3464 Z= 0.251 Angle : 0.638 6.502 4706 Z= 0.326 Chirality : 0.047 0.188 526 Planarity : 0.005 0.041 597 Dihedral : 5.847 49.429 549 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.11 % Allowed : 14.79 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.55 (0.40), residues: 420 helix: -2.19 (1.00), residues: 26 sheet: 1.10 (0.42), residues: 152 loop : -1.18 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 103 HIS 0.001 0.001 HIS L 90 PHE 0.010 0.001 PHE A 497 TYR 0.051 0.002 TYR A 453 ARG 0.002 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: H 110 THR cc_start: 0.8188 (p) cc_final: 0.7947 (p) REVERT: L 21 LEU cc_start: 0.8830 (mm) cc_final: 0.8523 (mp) REVERT: A 328 ARG cc_start: 0.7583 (tpt90) cc_final: 0.4992 (pmt-80) REVERT: A 360 ASN cc_start: 0.8881 (t0) cc_final: 0.8669 (t0) REVERT: A 392 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.6974 (m-80) REVERT: A 420 ASP cc_start: 0.6643 (m-30) cc_final: 0.5787 (t0) REVERT: A 458 LYS cc_start: 0.7436 (pttt) cc_final: 0.6710 (mmpt) REVERT: A 460 ASN cc_start: 0.6981 (m-40) cc_final: 0.6272 (m-40) outliers start: 15 outliers final: 12 residues processed: 81 average time/residue: 0.1770 time to fit residues: 17.0987 Evaluate side-chains 83 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.0770 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.0570 chunk 22 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.5256 ------------------------------------------------------------------------------- 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: 0.7989 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3464 Z= 0.207 Angle : 0.626 6.744 4706 Z= 0.317 Chirality : 0.047 0.150 526 Planarity : 0.005 0.040 597 Dihedral : 6.153 58.775 549 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.84 % Allowed : 14.79 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.41), residues: 420 helix: -2.19 (1.01), residues: 26 sheet: 1.11 (0.43), residues: 152 loop : -1.18 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 103 HIS 0.001 0.001 HIS A 519 PHE 0.007 0.001 PHE A 497 TYR 0.023 0.002 TYR L 49 ARG 0.007 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: H 110 THR cc_start: 0.8146 (p) cc_final: 0.7900 (p) REVERT: L 21 LEU cc_start: 0.8836 (mm) cc_final: 0.8518 (mp) REVERT: A 328 ARG cc_start: 0.7664 (tpt90) cc_final: 0.5071 (pmt-80) REVERT: A 392 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.6750 (m-80) REVERT: A 458 LYS cc_start: 0.7346 (pttt) cc_final: 0.6637 (mmpt) REVERT: A 465 GLU cc_start: 0.6847 (tt0) cc_final: 0.6295 (tt0) outliers start: 14 outliers final: 12 residues processed: 80 average time/residue: 0.1649 time to fit residues: 15.9762 Evaluate side-chains 86 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8013 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3464 Z= 0.260 Angle : 0.687 10.972 4706 Z= 0.347 Chirality : 0.048 0.150 526 Planarity : 0.005 0.042 597 Dihedral : 6.002 34.926 549 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.11 % Allowed : 14.79 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.68 (0.41), residues: 420 helix: -2.48 (0.95), residues: 26 sheet: 1.08 (0.43), residues: 152 loop : -1.30 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 103 HIS 0.001 0.001 HIS A 519 PHE 0.009 0.001 PHE A 486 TYR 0.024 0.002 TYR L 49 ARG 0.006 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 21 LEU cc_start: 0.8820 (mm) cc_final: 0.8486 (mp) REVERT: A 386 LYS cc_start: 0.4491 (mttt) cc_final: 0.3374 (mtpt) REVERT: A 392 PHE cc_start: 0.7404 (OUTLIER) cc_final: 0.6656 (m-80) REVERT: A 458 LYS cc_start: 0.7350 (pttt) cc_final: 0.6613 (mmpt) REVERT: A 465 GLU cc_start: 0.6889 (tt0) cc_final: 0.6311 (tt0) outliers start: 15 outliers final: 12 residues processed: 80 average time/residue: 0.1691 time to fit residues: 16.4110 Evaluate side-chains 85 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.0980 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.0370 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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: 0.7995 moved from start: 0.5379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3464 Z= 0.215 Angle : 0.675 8.895 4706 Z= 0.343 Chirality : 0.048 0.157 526 Planarity : 0.005 0.039 597 Dihedral : 6.069 49.013 549 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.56 % Allowed : 17.26 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.70 (0.41), residues: 420 helix: -2.48 (0.96), residues: 26 sheet: 1.08 (0.44), residues: 152 loop : -1.33 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.002 0.001 HIS A 519 PHE 0.008 0.001 PHE A 497 TYR 0.026 0.002 TYR L 49 ARG 0.006 0.001 ARG A 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: L 21 LEU cc_start: 0.8810 (mm) cc_final: 0.8470 (mp) REVERT: A 386 LYS cc_start: 0.4312 (mttt) cc_final: 0.3347 (mtpt) REVERT: A 392 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.6468 (m-80) REVERT: A 458 LYS cc_start: 0.7411 (pttt) cc_final: 0.6636 (mmpt) REVERT: A 465 GLU cc_start: 0.6867 (tt0) cc_final: 0.6326 (tt0) outliers start: 13 outliers final: 12 residues processed: 78 average time/residue: 0.1562 time to fit residues: 14.9164 Evaluate side-chains 85 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 23 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.0570 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.087564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.080516 restraints weight = 9545.762| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.70 r_work: 0.3292 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3464 Z= 0.189 Angle : 0.641 7.793 4706 Z= 0.326 Chirality : 0.047 0.157 526 Planarity : 0.005 0.038 597 Dihedral : 5.756 46.342 549 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.29 % Allowed : 18.36 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.67 (0.42), residues: 420 helix: -2.56 (0.92), residues: 26 sheet: 1.13 (0.45), residues: 152 loop : -1.32 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 98 HIS 0.003 0.001 HIS A 519 PHE 0.008 0.001 PHE A 497 TYR 0.025 0.002 TYR L 49 ARG 0.006 0.001 ARG A 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1481.38 seconds wall clock time: 27 minutes 14.69 seconds (1634.69 seconds total)