Starting phenix.real_space_refine on Sat Aug 3 00:54:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9t_37381/08_2024/8w9t_37381.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9t_37381/08_2024/8w9t_37381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9t_37381/08_2024/8w9t_37381.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9t_37381/08_2024/8w9t_37381.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9t_37381/08_2024/8w9t_37381.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9t_37381/08_2024/8w9t_37381.cif" } resolution = 2.6 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= 0.009 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: 5 Type Number sf(0) Gaussians S 46 5.16 5 Na 2 4.78 5 C 4324 2.51 5 N 1054 2.21 5 O 1148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "B TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B ARG 283": "NH1" <-> "NH2" Residue "B ARG 316": "NH1" <-> "NH2" Residue "B ARG 446": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6574 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3284 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 19, 'TRANS': 406} Chain breaks: 2 Chain: "B" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3284 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 19, 'TRANS': 406} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 4.42, per 1000 atoms: 0.67 Number of scatterers: 6574 At special positions: 0 Unit cell: (101.37, 84.63, 86.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 Na 2 11.00 O 1148 8.00 N 1054 7.00 C 4324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.3 seconds 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1588 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 0 sheets defined 76.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 42 through 65 removed outlier: 3.564A pdb=" N ALA A 55 " --> pdb=" O PHE A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 Processing helix chain 'A' and resid 101 through 116 Processing helix chain 'A' and resid 116 through 127 Processing helix chain 'A' and resid 179 through 216 removed outlier: 3.757A pdb=" N SER A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 227 Proline residue: A 222 - end of helix Processing helix chain 'A' and resid 229 through 244 Processing helix chain 'A' and resid 254 through 258 Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'A' and resid 277 through 293 removed outlier: 3.648A pdb=" N ARG A 283 " --> pdb=" O PRO A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 304 removed outlier: 4.060A pdb=" N THR A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 342 Processing helix chain 'A' and resid 344 through 348 removed outlier: 4.216A pdb=" N ASP A 348 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 367 removed outlier: 3.882A pdb=" N ARG A 367 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 379 Processing helix chain 'A' and resid 380 through 393 removed outlier: 3.528A pdb=" N LEU A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 427 Processing helix chain 'A' and resid 429 through 445 Processing helix chain 'A' and resid 445 through 452 Processing helix chain 'A' and resid 457 through 470 Processing helix chain 'A' and resid 479 through 485 Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 504 through 520 removed outlier: 3.525A pdb=" N LEU A 520 " --> pdb=" O LEU A 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 65 removed outlier: 3.563A pdb=" N ALA B 55 " --> pdb=" O PHE B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 88 Processing helix chain 'B' and resid 101 through 116 Processing helix chain 'B' and resid 116 through 127 Processing helix chain 'B' and resid 179 through 216 removed outlier: 3.756A pdb=" N SER B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 227 Proline residue: B 222 - end of helix Processing helix chain 'B' and resid 229 through 244 Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 277 through 293 removed outlier: 3.648A pdb=" N ARG B 283 " --> pdb=" O PRO B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 304 removed outlier: 4.060A pdb=" N THR B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 342 Processing helix chain 'B' and resid 344 through 348 removed outlier: 4.216A pdb=" N ASP B 348 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 367 removed outlier: 3.882A pdb=" N ARG B 367 " --> pdb=" O VAL B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 379 Processing helix chain 'B' and resid 380 through 393 removed outlier: 3.530A pdb=" N LEU B 393 " --> pdb=" O GLY B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 427 Processing helix chain 'B' and resid 429 through 445 Processing helix chain 'B' and resid 445 through 452 Processing helix chain 'B' and resid 457 through 470 Processing helix chain 'B' and resid 479 through 485 Processing helix chain 'B' and resid 498 through 503 Processing helix chain 'B' and resid 504 through 520 removed outlier: 3.526A pdb=" N LEU B 520 " --> pdb=" O LEU B 516 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.93 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1365 1.33 - 1.45: 1476 1.45 - 1.57: 3803 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 6718 Sorted by residual: bond pdb=" N VAL A 89 " pdb=" CA VAL A 89 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.25e-02 6.40e+03 4.55e+00 bond pdb=" CA ARG A 367 " pdb=" CB ARG A 367 " ideal model delta sigma weight residual 1.523 1.498 0.026 1.27e-02 6.20e+03 4.06e+00 bond pdb=" CA ARG B 367 " pdb=" CB ARG B 367 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.27e-02 6.20e+03 3.85e+00 bond pdb=" C SER B 90 " pdb=" O SER B 90 " ideal model delta sigma weight residual 1.235 1.212 0.023 1.23e-02 6.61e+03 3.47e+00 bond pdb=" CA ILE A 374 " pdb=" CB ILE A 374 " ideal model delta sigma weight residual 1.544 1.520 0.023 1.30e-02 5.92e+03 3.18e+00 ... (remaining 6713 not shown) Histogram of bond angle deviations from ideal: 98.94 - 105.95: 161 105.95 - 112.96: 3810 112.96 - 119.97: 2210 119.97 - 126.98: 2881 126.98 - 133.99: 72 Bond angle restraints: 9134 Sorted by residual: angle pdb=" N LEU A 87 " pdb=" CA LEU A 87 " pdb=" C LEU A 87 " ideal model delta sigma weight residual 111.28 115.08 -3.80 1.09e+00 8.42e-01 1.22e+01 angle pdb=" N LEU B 87 " pdb=" CA LEU B 87 " pdb=" C LEU B 87 " ideal model delta sigma weight residual 111.28 115.01 -3.73 1.09e+00 8.42e-01 1.17e+01 angle pdb=" N ILE A 374 " pdb=" CA ILE A 374 " pdb=" CB ILE A 374 " ideal model delta sigma weight residual 112.32 108.44 3.88 1.15e+00 7.56e-01 1.14e+01 angle pdb=" N SER B 90 " pdb=" CA SER B 90 " pdb=" C SER B 90 " ideal model delta sigma weight residual 112.04 107.41 4.63 1.44e+00 4.82e-01 1.04e+01 angle pdb=" N SER A 90 " pdb=" CA SER A 90 " pdb=" C SER A 90 " ideal model delta sigma weight residual 112.04 107.91 4.13 1.44e+00 4.82e-01 8.25e+00 ... (remaining 9129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.72: 3572 15.72 - 31.43: 304 31.43 - 47.15: 72 47.15 - 62.87: 6 62.87 - 78.59: 4 Dihedral angle restraints: 3958 sinusoidal: 1500 harmonic: 2458 Sorted by residual: dihedral pdb=" CA ARG A 367 " pdb=" C ARG A 367 " pdb=" N HIS A 368 " pdb=" CA HIS A 368 " ideal model delta harmonic sigma weight residual 180.00 158.03 21.97 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ARG B 367 " pdb=" C ARG B 367 " pdb=" N HIS B 368 " pdb=" CA HIS B 368 " ideal model delta harmonic sigma weight residual 180.00 158.16 21.84 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ASN B 365 " pdb=" C ASN B 365 " pdb=" N ALA B 366 " pdb=" CA ALA B 366 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 3955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 780 0.041 - 0.081: 264 0.081 - 0.122: 56 0.122 - 0.163: 7 0.163 - 0.203: 3 Chirality restraints: 1110 Sorted by residual: chirality pdb=" CA ILE A 374 " pdb=" N ILE A 374 " pdb=" C ILE A 374 " pdb=" CB ILE A 374 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ASN A 253 " pdb=" N ASN A 253 " pdb=" C ASN A 253 " pdb=" CB ASN A 253 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" CA ASN B 253 " pdb=" N ASN B 253 " pdb=" C ASN B 253 " pdb=" CB ASN B 253 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.90e-01 ... (remaining 1107 not shown) Planarity restraints: 1108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 88 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.00e+00 pdb=" C THR A 88 " 0.046 2.00e-02 2.50e+03 pdb=" O THR A 88 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL A 89 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 252 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.08e+00 pdb=" C GLU B 252 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU B 252 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN B 253 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 252 " -0.012 2.00e-02 2.50e+03 2.45e-02 6.03e+00 pdb=" C GLU A 252 " 0.042 2.00e-02 2.50e+03 pdb=" O GLU A 252 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN A 253 " -0.014 2.00e-02 2.50e+03 ... (remaining 1105 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 83 2.65 - 3.21: 6554 3.21 - 3.78: 10886 3.78 - 4.34: 15511 4.34 - 4.90: 24867 Nonbonded interactions: 57901 Sorted by model distance: nonbonded pdb=" O GLN B 424 " pdb=" OG1 THR B 527 " model vdw 2.090 3.040 nonbonded pdb=" O GLN A 424 " pdb=" OG1 THR A 527 " model vdw 2.091 3.040 nonbonded pdb=" NH2 ARG A 367 " pdb=" O PRO A 394 " model vdw 2.189 3.120 nonbonded pdb=" NH2 ARG B 367 " pdb=" O PRO B 394 " model vdw 2.189 3.120 nonbonded pdb=" O GLY B 91 " pdb=" O HOH B 801 " model vdw 2.257 3.040 ... (remaining 57896 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.570 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.080 Process input model: 23.170 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:13.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 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 : 0.005 0.032 6718 Z= 0.285 Angle : 0.601 6.685 9134 Z= 0.333 Chirality : 0.043 0.203 1110 Planarity : 0.005 0.041 1108 Dihedral : 12.297 78.585 2370 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.67 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.25), residues: 840 helix: -0.90 (0.18), residues: 582 sheet: None (None), residues: 0 loop : -1.73 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 287 HIS 0.007 0.002 HIS B 368 PHE 0.011 0.001 PHE A 361 TYR 0.015 0.002 TYR B 50 ARG 0.004 0.000 ARG B 450 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.693 Fit side-chains REVERT: A 69 ASN cc_start: 0.7256 (t0) cc_final: 0.7047 (t0) REVERT: A 300 LEU cc_start: 0.7012 (mt) cc_final: 0.6743 (mm) REVERT: A 447 ARG cc_start: 0.6932 (mtp85) cc_final: 0.6616 (ttp-110) REVERT: B 300 LEU cc_start: 0.7012 (mt) cc_final: 0.6742 (mm) REVERT: B 447 ARG cc_start: 0.6940 (mtp85) cc_final: 0.6620 (ttp-110) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 1.1529 time to fit residues: 123.9870 Evaluate side-chains 75 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN A 260 ASN A 270 GLN A 312 ASN A 358 ASN A 368 HIS A 484 HIS B 69 ASN B 253 ASN B 260 ASN B 270 GLN B 309 HIS B 312 ASN B 358 ASN B 368 HIS B 484 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6718 Z= 0.229 Angle : 0.555 6.280 9134 Z= 0.293 Chirality : 0.041 0.149 1110 Planarity : 0.005 0.042 1108 Dihedral : 4.570 21.429 896 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.13 % Allowed : 9.60 % Favored : 88.27 % 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: 0.21 (0.27), residues: 840 helix: 0.77 (0.20), residues: 586 sheet: None (None), residues: 0 loop : -1.24 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 287 HIS 0.007 0.002 HIS A 368 PHE 0.011 0.002 PHE B 463 TYR 0.015 0.002 TYR B 50 ARG 0.003 0.001 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 0.827 Fit side-chains REVERT: A 447 ARG cc_start: 0.6757 (mtp85) cc_final: 0.6397 (ttp-110) REVERT: B 447 ARG cc_start: 0.6758 (mtp85) cc_final: 0.6396 (ttp-110) outliers start: 16 outliers final: 5 residues processed: 110 average time/residue: 0.9871 time to fit residues: 115.4003 Evaluate side-chains 83 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6718 Z= 0.251 Angle : 0.564 7.179 9134 Z= 0.295 Chirality : 0.041 0.152 1110 Planarity : 0.004 0.043 1108 Dihedral : 4.581 22.231 896 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.53 % Allowed : 10.80 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.28), residues: 840 helix: 1.39 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -1.09 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 287 HIS 0.005 0.001 HIS A 368 PHE 0.011 0.002 PHE B 463 TYR 0.014 0.002 TYR A 76 ARG 0.003 0.001 ARG B 367 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 0.672 Fit side-chains REVERT: A 256 ILE cc_start: 0.8326 (tt) cc_final: 0.8104 (tt) REVERT: A 447 ARG cc_start: 0.6763 (mtp85) cc_final: 0.6444 (ttp-110) REVERT: B 256 ILE cc_start: 0.8330 (tt) cc_final: 0.8108 (tt) REVERT: B 447 ARG cc_start: 0.6763 (mtp85) cc_final: 0.6444 (ttp-110) outliers start: 19 outliers final: 10 residues processed: 105 average time/residue: 1.1352 time to fit residues: 125.8581 Evaluate side-chains 96 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6718 Z= 0.232 Angle : 0.545 7.093 9134 Z= 0.285 Chirality : 0.041 0.144 1110 Planarity : 0.004 0.043 1108 Dihedral : 4.506 21.538 896 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.67 % Allowed : 12.53 % Favored : 84.80 % 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: 1.35 (0.28), residues: 840 helix: 1.71 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -1.04 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 287 HIS 0.006 0.001 HIS B 368 PHE 0.010 0.001 PHE A 463 TYR 0.014 0.002 TYR B 50 ARG 0.002 0.001 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.739 Fit side-chains REVERT: A 256 ILE cc_start: 0.8303 (tt) cc_final: 0.8068 (tt) REVERT: A 300 LEU cc_start: 0.6817 (mt) cc_final: 0.6586 (mm) REVERT: A 447 ARG cc_start: 0.6768 (mtp85) cc_final: 0.6458 (ttp-110) REVERT: B 256 ILE cc_start: 0.8305 (tt) cc_final: 0.8071 (tt) REVERT: B 300 LEU cc_start: 0.6817 (mt) cc_final: 0.6585 (mm) REVERT: B 447 ARG cc_start: 0.6763 (mtp85) cc_final: 0.6455 (ttp-110) outliers start: 20 outliers final: 12 residues processed: 111 average time/residue: 1.0990 time to fit residues: 129.0298 Evaluate side-chains 102 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.0870 chunk 69 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 20 optimal weight: 7.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6718 Z= 0.133 Angle : 0.472 6.158 9134 Z= 0.246 Chirality : 0.038 0.132 1110 Planarity : 0.004 0.041 1108 Dihedral : 3.975 15.952 896 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.00 % Allowed : 14.13 % Favored : 83.87 % 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: 2.15 (0.29), residues: 840 helix: 2.39 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.92 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 531 HIS 0.003 0.001 HIS A 368 PHE 0.011 0.001 PHE B 198 TYR 0.015 0.002 TYR B 50 ARG 0.001 0.000 ARG A 448 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 0.692 Fit side-chains REVERT: A 256 ILE cc_start: 0.8261 (tt) cc_final: 0.8030 (tt) REVERT: A 447 ARG cc_start: 0.6868 (mtp85) cc_final: 0.6599 (ttp-110) REVERT: A 529 LYS cc_start: 0.6374 (ptmm) cc_final: 0.6075 (pttp) REVERT: B 256 ILE cc_start: 0.8263 (tt) cc_final: 0.8031 (tt) REVERT: B 447 ARG cc_start: 0.6872 (mtp85) cc_final: 0.6601 (ttp-110) REVERT: B 529 LYS cc_start: 0.6331 (ptmm) cc_final: 0.5997 (pttp) outliers start: 15 outliers final: 10 residues processed: 108 average time/residue: 1.1303 time to fit residues: 128.8197 Evaluate side-chains 101 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 47 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6718 Z= 0.145 Angle : 0.479 6.157 9134 Z= 0.250 Chirality : 0.038 0.120 1110 Planarity : 0.004 0.041 1108 Dihedral : 3.979 16.739 896 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.13 % Allowed : 15.47 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.29), residues: 840 helix: 2.57 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.85 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 502 HIS 0.004 0.001 HIS B 368 PHE 0.011 0.001 PHE B 198 TYR 0.015 0.002 TYR A 81 ARG 0.006 0.000 ARG B 367 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.794 Fit side-chains REVERT: A 57 LEU cc_start: 0.8083 (mt) cc_final: 0.7505 (tp) REVERT: A 307 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.5956 (mm-30) REVERT: A 447 ARG cc_start: 0.6889 (mtp85) cc_final: 0.6628 (ttp-110) REVERT: B 57 LEU cc_start: 0.8086 (mt) cc_final: 0.7507 (tp) REVERT: B 307 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.5949 (mm-30) REVERT: B 447 ARG cc_start: 0.6892 (mtp85) cc_final: 0.6628 (ttp-110) outliers start: 16 outliers final: 11 residues processed: 98 average time/residue: 1.1428 time to fit residues: 118.2427 Evaluate side-chains 101 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 68 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6718 Z= 0.137 Angle : 0.479 5.982 9134 Z= 0.247 Chirality : 0.038 0.115 1110 Planarity : 0.004 0.041 1108 Dihedral : 3.883 15.199 896 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.27 % Allowed : 15.07 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.29), residues: 840 helix: 2.70 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.80 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 502 HIS 0.004 0.001 HIS A 368 PHE 0.011 0.001 PHE A 198 TYR 0.015 0.002 TYR A 81 ARG 0.007 0.000 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 0.785 Fit side-chains REVERT: A 57 LEU cc_start: 0.8139 (mt) cc_final: 0.7557 (tp) REVERT: A 307 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.5969 (mm-30) REVERT: A 447 ARG cc_start: 0.6870 (mtp85) cc_final: 0.6617 (ttp-110) REVERT: A 529 LYS cc_start: 0.6258 (ptmm) cc_final: 0.5664 (ttmm) REVERT: B 57 LEU cc_start: 0.8140 (mt) cc_final: 0.7555 (tp) REVERT: B 307 GLU cc_start: 0.6428 (OUTLIER) cc_final: 0.5967 (mm-30) REVERT: B 447 ARG cc_start: 0.6878 (mtp85) cc_final: 0.6619 (ttp-110) REVERT: B 529 LYS cc_start: 0.6289 (ptmm) cc_final: 0.5703 (ttmm) outliers start: 17 outliers final: 8 residues processed: 97 average time/residue: 1.1135 time to fit residues: 114.0921 Evaluate side-chains 96 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 55 optimal weight: 0.0470 chunk 40 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 HIS ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6718 Z= 0.159 Angle : 0.494 6.174 9134 Z= 0.254 Chirality : 0.039 0.119 1110 Planarity : 0.004 0.041 1108 Dihedral : 3.995 16.736 896 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.27 % Allowed : 15.73 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.29), residues: 840 helix: 2.66 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.78 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 502 HIS 0.005 0.001 HIS B 368 PHE 0.010 0.001 PHE B 198 TYR 0.014 0.002 TYR A 81 ARG 0.007 0.001 ARG B 367 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.745 Fit side-chains REVERT: A 57 LEU cc_start: 0.8102 (mt) cc_final: 0.7524 (tp) REVERT: A 256 ILE cc_start: 0.8309 (tt) cc_final: 0.8081 (tt) REVERT: A 307 GLU cc_start: 0.6456 (OUTLIER) cc_final: 0.5930 (mm-30) REVERT: A 447 ARG cc_start: 0.6873 (mtp85) cc_final: 0.6599 (ttp-110) REVERT: A 529 LYS cc_start: 0.6397 (ptmm) cc_final: 0.5791 (ttmm) REVERT: B 57 LEU cc_start: 0.8103 (mt) cc_final: 0.7521 (tp) REVERT: B 256 ILE cc_start: 0.8312 (tt) cc_final: 0.8085 (tt) REVERT: B 307 GLU cc_start: 0.6456 (OUTLIER) cc_final: 0.5936 (mm-30) REVERT: B 447 ARG cc_start: 0.6848 (mtp85) cc_final: 0.6574 (ttp-110) REVERT: B 529 LYS cc_start: 0.6393 (ptmm) cc_final: 0.5793 (ttmm) outliers start: 17 outliers final: 12 residues processed: 96 average time/residue: 1.1391 time to fit residues: 115.5008 Evaluate side-chains 99 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 HIS ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6718 Z= 0.176 Angle : 0.511 6.294 9134 Z= 0.263 Chirality : 0.039 0.123 1110 Planarity : 0.004 0.041 1108 Dihedral : 4.103 17.663 896 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.40 % Allowed : 14.93 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.29), residues: 840 helix: 2.54 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.76 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 502 HIS 0.005 0.001 HIS A 368 PHE 0.010 0.001 PHE A 198 TYR 0.015 0.002 TYR B 76 ARG 0.006 0.001 ARG B 367 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 0.810 Fit side-chains REVERT: A 57 LEU cc_start: 0.8110 (mt) cc_final: 0.7524 (tp) REVERT: A 256 ILE cc_start: 0.8302 (tt) cc_final: 0.8060 (tt) REVERT: A 307 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.5941 (mm-30) REVERT: A 447 ARG cc_start: 0.6767 (mtp85) cc_final: 0.6503 (ttp-110) REVERT: A 529 LYS cc_start: 0.6462 (ptmm) cc_final: 0.6040 (pttp) REVERT: B 57 LEU cc_start: 0.8112 (mt) cc_final: 0.7524 (tp) REVERT: B 256 ILE cc_start: 0.8306 (tt) cc_final: 0.8064 (tt) REVERT: B 307 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.5947 (mm-30) REVERT: B 447 ARG cc_start: 0.6781 (mtp85) cc_final: 0.6510 (ttp-110) REVERT: B 529 LYS cc_start: 0.6453 (ptmm) cc_final: 0.6034 (pttp) outliers start: 18 outliers final: 14 residues processed: 98 average time/residue: 1.1212 time to fit residues: 116.2840 Evaluate side-chains 100 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 0.0070 chunk 83 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 HIS ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6718 Z= 0.163 Angle : 0.502 6.168 9134 Z= 0.258 Chirality : 0.039 0.120 1110 Planarity : 0.004 0.041 1108 Dihedral : 4.063 17.245 896 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.27 % Allowed : 14.80 % Favored : 82.93 % 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: 2.43 (0.29), residues: 840 helix: 2.57 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.74 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 502 HIS 0.005 0.001 HIS B 368 PHE 0.010 0.001 PHE A 198 TYR 0.015 0.002 TYR B 81 ARG 0.006 0.000 ARG B 367 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 0.771 Fit side-chains REVERT: A 57 LEU cc_start: 0.8091 (mt) cc_final: 0.7503 (tp) REVERT: A 256 ILE cc_start: 0.8296 (tt) cc_final: 0.8055 (tt) REVERT: A 307 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.6000 (mm-30) REVERT: A 447 ARG cc_start: 0.6803 (mtp85) cc_final: 0.6533 (ttp-110) REVERT: A 529 LYS cc_start: 0.6447 (ptmm) cc_final: 0.5843 (ttmm) REVERT: B 57 LEU cc_start: 0.8091 (mt) cc_final: 0.7505 (tp) REVERT: B 256 ILE cc_start: 0.8303 (tt) cc_final: 0.8060 (tt) REVERT: B 307 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.6008 (mm-30) REVERT: B 447 ARG cc_start: 0.6797 (mtp85) cc_final: 0.6525 (ttp-110) REVERT: B 529 LYS cc_start: 0.6433 (ptmm) cc_final: 0.5835 (ttmm) outliers start: 17 outliers final: 14 residues processed: 97 average time/residue: 1.1726 time to fit residues: 120.1847 Evaluate side-chains 96 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 58 optimal weight: 0.0370 chunk 3 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.147152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.128755 restraints weight = 7970.533| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.28 r_work: 0.3375 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6718 Z= 0.124 Angle : 0.466 5.747 9134 Z= 0.241 Chirality : 0.038 0.114 1110 Planarity : 0.004 0.040 1108 Dihedral : 3.805 15.677 896 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.87 % Allowed : 15.73 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.29), residues: 840 helix: 2.81 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.71 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 531 HIS 0.003 0.001 HIS A 368 PHE 0.011 0.001 PHE A 198 TYR 0.017 0.002 TYR A 81 ARG 0.004 0.000 ARG A 367 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2503.06 seconds wall clock time: 44 minutes 42.93 seconds (2682.93 seconds total)